trio_phasing_results

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Last updated: 2025-07-22

Checks: 7 0

Knit directory: phasing_clean/

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Repository version: 8298e64

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Unstaged changes:
    Modified:   code/batch_annotate_trio_switch.sh
    Modified:   code/batch_compare_trio.sh
    Modified:   code/batch_phase_sd.sh
    Modified:   code/batch_phase_trio.sh
    Modified:   code/trio_phase_results.R

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/trio_phasing_results.Rmd) and HTML (docs/trio_phasing_results.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

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---

Introduction

Here in this document we present figures, tables, and statistics for the phasing evaluation on the autosomes. This sample consists of 602 individuals phased using a reference panel of unrelated individuals from the 1000 genomes project. The phasing results are compared to a pedigree-adjusted phased genome for each sample.

Libraries and Data

library(tidyverse)
library(pander)
library(reactable)
library(yaml)
library(gtsummary)

library(grid)
library(gridExtra) 

config_obj <- yaml::read_yaml("_config.yaml")

cbPalette <- c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7")

df_subj <- read_csv("data/1kgp/subject_info.csv")
ped_df <- read_table("data/1kgp/1kGP.3202_samples.pedigree_info.txt")

child_ids <- ped_df %>% filter(fatherID != "0" & motherID != "0") %>% pull(sampleID)
unrel_ids <- scan("data/1kgp/unrelated_subjects.txt", what = character())

df_subj_rel <- df_subj %>%
  filter(SAMPLE_NAME %in% child_ids)
df_subj_rel$id2 <- 1:602

df_subj_unrel <- df_subj %>%
  filter(SAMPLE_NAME %in% unrel_ids)

Switch Error Summaries

df_switch_trio <- vector(mode = "list", length = 22)


for(i in 1:22){
  df_switch_trio[[i]] <- read_csv(paste0(config_obj$base_dir, "/output/trio_phase_", i, "/switch_errors/summary.csv"),
                                  show_col_types = FALSE)
}

And let’s also load the results from when we phase without the triple heterozygous positions:

df_switch_trio_noth <- read_csv("output/all_noTH.csv", show_col_types = F)

Heterozygous Position Counts

# het dfs
df_het <- vector(mode = "list", length = 22)

for(i in 1:22){
  df_het[[i]] <- read_tsv(paste0(config_obj$base_dir, "/output/trio_phase_", i, "/no_th/het_pos_count.tsv"),
                   col_names = c("id", "n_het"), 
                   show_col_types = FALSE)
}

deCODE genetic maps (cM/MB)

df_decode <- vector(mode = "list", length = 22)

for(i in 1:22){
  df_decode[[i]] <- read_tsv(paste0("data/decode/chr", i, "_recomb.bed"), col_names = c("chr", "start", "end", "cM_MB"), show_col_types = FALSE)
}

Chr X Results

We’ll also pull in the results on chromosome X for the synthetic diploids to allow for comparisons of rates between 15 and X.

sd_pair_info_df <- read_delim("data/sample_pairs.csv", col_names = c("POP", "ID1", "ID2"))

Rows: 1000 Columns: 3
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (3): POP, ID1, ID2

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

sd_pair_info_df <- left_join(sd_pair_info_df, df_subj, by = c("ID1"="SAMPLE_NAME")) %>%
  rename(SP = SUPER) %>%
  select(-POPULATION)

df_switch_x <- read_csv(paste0(config_obj$base_dir,"/output/switch_errors/switch_errors/summary.csv"))

Rows: 1000 Columns: 45
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr  (2): pop, subpop
dbl (43): pair_id, n_switch_eagle, n_switch_beagle, n_switch_shapeit, n_flip...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

df_het_x <- read_tsv(paste0(config_obj$base_dir, "/output/switch_errors/het_pos_count.tsv"), col_names = c("id", "n_het"))

Rows: 1000 Columns: 2
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
dbl (2): id, n_het

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

n_var_site_x <- 1722954
df_het_x$frac_het <- df_het_x$n_het / n_var_site_x

sd_pair_info_df$n_het <-df_het_x$n_het
sd_pair_info_df$frac_het <-df_het_x$frac_het

df_decode_x <- read_tsv("data/decode/chrX_recomb.bed", col_names = c("chr", "start", "end", "cM_MB"))

Rows: 23976 Columns: 4
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (1): chr
dbl (3): start, end, cM_MB

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

Subject Information

The 1000 Genomes collection of 3,202 genomes is sampled from 26 different populations, each belonging to 1 of 5 distinct super-populations (AFR, AMR, EAS, EUR, SAS). All 26 populations are represented in the 2,504 1kGP phase 3 subjects, but not all are present in the 602 trios sequenced by the New York Genome Center:

df_subj %>%
  group_by(SUPER, POPULATION) %>%
  summarize(N = n()) %>%
  reactable( 
            groupBy = c("SUPER"),
            columns = list(
              N = colDef(aggregate = "sum")),
    bordered = TRUE,
    defaultExpanded = TRUE)

`summarise()` has grouped output by 'SUPER'. You can override using the
`.groups` argument.

df_subj_rel %>%
  group_by(SUPER, POPULATION) %>%
  summarize(N = n()) %>%
  reactable( 
            groupBy = c("SUPER"),
            columns = list(
              N = colDef(aggregate = "sum")),
    bordered = TRUE,
    defaultExpanded = TRUE)

`summarise()` has grouped output by 'SUPER'. You can override using the
`.groups` argument.

df_subj_unrel %>%
  group_by(SUPER, POPULATION) %>%
  summarize(N = n()) %>%
  reactable( 
            groupBy = c("SUPER"),
            columns = list(
              N = colDef(aggregate = "sum")),
    bordered = TRUE,
    defaultExpanded = TRUE)

`summarise()` has grouped output by 'SUPER'. You can override using the
`.groups` argument.

For completeness, we also tabulate other summary information about the 602 trios (which is just sex; 1 - male, 2 - female):

df_subj_rel %>%
  group_by(sex) %>%
  summarize(N = n()) %>%
  reactable( 
            groupBy = c("sex"),
            columns = list(
              N = colDef(aggregate = "sum")),
    bordered = TRUE,
    defaultExpanded = TRUE)

df_subj_unrel %>%
  group_by(sex) %>%
  summarize(N = n()) %>%
  reactable( 
            groupBy = c("sex"),
            columns = list(
              N = colDef(aggregate = "sum")),
    bordered = TRUE,
    defaultExpanded = TRUE)

All Autosome Summaries

Total Errors

First let’s get an overall error rate across all 22 autosomes based on our re-phasing of the trio probands:

df_total <- df_switch_trio[[1]] %>%
  mutate(Eagle = (n_other_eagle + n_flip_eagle) / n_hets,
         Beagle = (n_other_beagle + n_flip_beagle) / n_hets,
         SHAPEIT = (n_other_shapeit + n_flip_shapeit) / n_hets) %>%
  select(Eagle, Beagle, SHAPEIT, SUPER, pair_id) %>%
  mutate(chrom = 1)

df_total_noth <- df_switch_trio_noth %>%
  mutate(Eagle = (n_switch_e + n_flip_e) / n_het,
         Beagle = (n_switch_b + n_flip_b) / n_het,
         SHAPEIT = (n_switch_s + n_flip_s) / n_het) %>%
  select(Eagle, Beagle, SHAPEIT, sample, chrom)

df_total_noth <- df_total_noth %>%
  left_join({df_subj_rel %>% select(id2, SUPER)}, by = c("sample" = "id2")) %>%
  rename(pair_id = sample) %>%
  select(Eagle, Beagle, SHAPEIT, SUPER, pair_id, chrom)

for(i in 2:22){
  df_total <- bind_rows(df_total, 
                        {
                          df_switch_trio[[i]] %>%
                            mutate(Eagle = (n_other_eagle + n_flip_eagle) / n_hets,
                                   Beagle = (n_other_beagle + n_flip_beagle) / n_hets,
                                   SHAPEIT = (n_other_shapeit + n_flip_shapeit) / n_hets) %>%
                            select(Eagle, Beagle, SHAPEIT, SUPER, pair_id) %>%
                            mutate(chrom = i)
                        })
}

df_total <- df_total %>%
  bind_rows({df_switch_x %>%
      mutate(Eagle = (n_other_eagle + n_flip_eagle) / n_hets,
                                   Beagle = (n_other_beagle + n_flip_beagle) / n_hets,
                                   SHAPEIT = (n_other_shapeit + n_flip_shapeit) / n_hets) %>%
      rename(SUPER = pop) %>%
                            select(Eagle, Beagle, SHAPEIT, SUPER) %>%
                            mutate(pair_id = 603:1602, chrom = 23)})

df_total_noth <- df_total_noth %>%
  bind_rows({df_switch_x %>%
      mutate(Eagle = (n_other_eagle + n_flip_eagle) / n_hets,
                                   Beagle = (n_other_beagle + n_flip_beagle) / n_hets,
                                   SHAPEIT = (n_other_shapeit + n_flip_shapeit) / n_hets) %>%
      rename(SUPER = pop) %>%
                            select(Eagle, Beagle, SHAPEIT, SUPER) %>%
                            mutate(pair_id = 603:1602, chrom = 23)})

Total Error Rates: with TH

df_total %>%
  group_by(chrom) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>%
  knitr::kable()

chrom	Beagle	Eagle	SHAPEIT
1	0.0067395	0.0067223	0.0071348
2	0.0067182	0.0066709	0.0071241
3	0.0062862	0.0062368	0.0066700
4	0.0058272	0.0058086	0.0061830
5	0.0062772	0.0062116	0.0066640
6	0.0056205	0.0056106	0.0059695
7	0.0066444	0.0066400	0.0070178
8	0.0016721	0.0022869	0.0017815
9	0.0079744	0.0079202	0.0083190
10	0.0064289	0.0064593	0.0068026
11	0.0063130	0.0062888	0.0066795
12	0.0064549	0.0064011	0.0068462
13	0.0062073	0.0061843	0.0065682
14	0.0069985	0.0070401	0.0074116
15	0.0080919	0.0081443	0.0085070
16	0.0080883	0.0081102	0.0085211
17	0.0082995	0.0083780	0.0086566
18	0.0066549	0.0066279	0.0070294
19	0.0077351	0.0078323	0.0080561
20	0.0080259	0.0080467	0.0083414
21	0.0086549	0.0088189	0.0090797
22	0.0098210	0.0100373	0.0101722
23	0.0030794	0.0036645	0.0031251

df_total %>%
  group_by(chrom, SUPER) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>% 
  knitr::kable()

`summarise()` has grouped output by 'chrom'. You can override using the
`.groups` argument.

chrom	SUPER	Beagle	Eagle	SHAPEIT
1	AFR	0.0055470	0.0052014	0.0058600
1	AMR	0.0064375	0.0065297	0.0068945
1	EAS	0.0092799	0.0096876	0.0097752
1	EUR	0.0062678	0.0063948	0.0065600
1	SAS	0.0084880	0.0085297	0.0090237
2	AFR	0.0054907	0.0051472	0.0058282
2	AMR	0.0066014	0.0066504	0.0070537
2	EAS	0.0092474	0.0095998	0.0098008
2	EUR	0.0060698	0.0061718	0.0063560
2	SAS	0.0084829	0.0084545	0.0090015
3	AFR	0.0051191	0.0047501	0.0054396
3	AMR	0.0060628	0.0061345	0.0065287
3	EAS	0.0087136	0.0090203	0.0091782
3	EUR	0.0058531	0.0059451	0.0060974
3	SAS	0.0078949	0.0079269	0.0084038
4	AFR	0.0047064	0.0043872	0.0049933
4	AMR	0.0058144	0.0058702	0.0062470
4	EAS	0.0078453	0.0082126	0.0082989
4	EUR	0.0053370	0.0054733	0.0055894
4	SAS	0.0074061	0.0074566	0.0078482
5	AFR	0.0051628	0.0047968	0.0055004
5	AMR	0.0060247	0.0060731	0.0064754
5	EAS	0.0086690	0.0089300	0.0091428
5	EUR	0.0057598	0.0058361	0.0060024
5	SAS	0.0079450	0.0079505	0.0084528
6	AFR	0.0046691	0.0044083	0.0049870
6	AMR	0.0054834	0.0055737	0.0058509
6	EAS	0.0076252	0.0079459	0.0080756
6	EUR	0.0050195	0.0050966	0.0052602
6	SAS	0.0071493	0.0071820	0.0075932
7	AFR	0.0056451	0.0053659	0.0059259
7	AMR	0.0063283	0.0064342	0.0068119
7	EAS	0.0089896	0.0092754	0.0094416
7	EUR	0.0060694	0.0061896	0.0063094
7	SAS	0.0082539	0.0083194	0.0087699
8	AFR	0.0017555	0.0020756	0.0018302
8	AMR	0.0023261	0.0029894	0.0024296
8	EAS	0.0007489	0.0019593	0.0007036
8	EUR	0.0011225	0.0018524	0.0012282
8	SAS	0.0018944	0.0024787	0.0022310
9	AFR	0.0068396	0.0064942	0.0071230
9	AMR	0.0075185	0.0075597	0.0079218
9	EAS	0.0107378	0.0110860	0.0111549
9	EUR	0.0074135	0.0075191	0.0076602
9	SAS	0.0097581	0.0096966	0.0102146
10	AFR	0.0053702	0.0051045	0.0056988
10	AMR	0.0061843	0.0063284	0.0065907
10	EAS	0.0086799	0.0090581	0.0091298
10	EUR	0.0058815	0.0060049	0.0061312
10	SAS	0.0081091	0.0082448	0.0086279
11	AFR	0.0051038	0.0047643	0.0054421
11	AMR	0.0061504	0.0062567	0.0065811
11	EAS	0.0087048	0.0089563	0.0091293
11	EUR	0.0057273	0.0058646	0.0059475
11	SAS	0.0081458	0.0082203	0.0086106
12	AFR	0.0052336	0.0048435	0.0055285
12	AMR	0.0061647	0.0062722	0.0066160
12	EAS	0.0088507	0.0091833	0.0092980
12	EUR	0.0058835	0.0059865	0.0061495
12	SAS	0.0085005	0.0084572	0.0091331
13	AFR	0.0051338	0.0047588	0.0054669
13	AMR	0.0058467	0.0059489	0.0062847
13	EAS	0.0086166	0.0089850	0.0089645
13	EUR	0.0056813	0.0058049	0.0059074
13	SAS	0.0079485	0.0080400	0.0084311
14	AFR	0.0058491	0.0055279	0.0061819
14	AMR	0.0069236	0.0070836	0.0073920
14	EAS	0.0092338	0.0097126	0.0097585
14	EUR	0.0063719	0.0065804	0.0066770
14	SAS	0.0087328	0.0088611	0.0092879
15	AFR	0.0069205	0.0067038	0.0072805
15	AMR	0.0075491	0.0076851	0.0080371
15	EAS	0.0107938	0.0112109	0.0112988
15	EUR	0.0075873	0.0077744	0.0078511
15	SAS	0.0100833	0.0101590	0.0106255
16	AFR	0.0067101	0.0064605	0.0070518
16	AMR	0.0077841	0.0078624	0.0082867
16	EAS	0.0110409	0.0114166	0.0115555
16	EUR	0.0074827	0.0076739	0.0078211
16	SAS	0.0100990	0.0101592	0.0106840
17	AFR	0.0070385	0.0068052	0.0073412
17	AMR	0.0078579	0.0080042	0.0082180
17	EAS	0.0114246	0.0118422	0.0119096
17	EUR	0.0075552	0.0077852	0.0078145
17	SAS	0.0102826	0.0105113	0.0107783
18	AFR	0.0053748	0.0050216	0.0056865
18	AMR	0.0064686	0.0065122	0.0068916
18	EAS	0.0092433	0.0096255	0.0096967
18	EUR	0.0061722	0.0063152	0.0063982
18	SAS	0.0083972	0.0084671	0.0089623
19	AFR	0.0065154	0.0064078	0.0067781
19	AMR	0.0073732	0.0075864	0.0077798
19	EAS	0.0107155	0.0110315	0.0110440
19	EUR	0.0070417	0.0072541	0.0072739
19	SAS	0.0095512	0.0096150	0.0099775
20	AFR	0.0064594	0.0062060	0.0066644
20	AMR	0.0078739	0.0079705	0.0082688
20	EAS	0.0114298	0.0117419	0.0118613
20	EUR	0.0072520	0.0074422	0.0075192
20	SAS	0.0100663	0.0101533	0.0104775
21	AFR	0.0079544	0.0078804	0.0083141
21	AMR	0.0082498	0.0085883	0.0088090
21	EAS	0.0106827	0.0110631	0.0110567
21	EUR	0.0079347	0.0081427	0.0082329
21	SAS	0.0101535	0.0103601	0.0107176
22	AFR	0.0087059	0.0086329	0.0089909
22	AMR	0.0094276	0.0097295	0.0097832
22	EAS	0.0126112	0.0132342	0.0130122
22	EUR	0.0090470	0.0093067	0.0093290
22	SAS	0.0117030	0.0120662	0.0122487
23	AFR	0.0018961	0.0023549	0.0019652
23	AMR	0.0023216	0.0027562	0.0024143
23	EAS	0.0047907	0.0056040	0.0047650
23	EUR	0.0027532	0.0032940	0.0028181
23	SAS	0.0036354	0.0043134	0.0036627

df_total %>%
  group_by(chrom) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>%
  pivot_longer(Beagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  ggplot(aes(x = chrom, y = error_rate, colour = method, shape = method)) +
  geom_point(size=3) +
  theme_bw() +
  xlab("Chromosome") +
  ylab("Error Rate") +
  labs(colour = "Method", shape = "Method") +
  scale_colour_brewer(palette = "Set2") +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5)) +
  scale_x_continuous("Chromosome", labels = as.character(unique(df_total$chrom)), breaks = unique(df_total$chrom))

Past versions of unnamed-chunk-10-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
cb6aa66	Andy Beck	2024-06-06
17d41d5	Andy Beck	2024-05-22
d7d8f5a	Andy Beck	2024-05-22
da672c2	Andy Beck	2024-05-22
4255fdf	Andy Beck	2024-05-21

df_total %>%
  group_by(chrom, SUPER) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>%
  pivot_longer(Beagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  ggplot(aes(x = chrom, y = error_rate, colour = SUPER, shape = method)) +
  geom_point(size=2) +
  theme_bw() +
  ylab("Error Rate") +
  xlab("Chromosome") +
  labs(colour = "Population", shape = "Method") +
  scale_colour_brewer(palette = "Set1")

`summarise()` has grouped output by 'chrom'. You can override using the
`.groups` argument.

Past versions of unnamed-chunk-10-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
cb6aa66	Andy Beck	2024-06-06
17d41d5	Andy Beck	2024-05-22
d7d8f5a	Andy Beck	2024-05-22
da672c2	Andy Beck	2024-05-22
4255fdf	Andy Beck	2024-05-21

Total Error Rates: without TH

df_total_noth %>%
  group_by(chrom) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>%
  knitr::kable()

chrom	Beagle	Eagle	SHAPEIT
1	0.0076521	0.0074991	0.0081145
2	0.0076647	0.0074667	0.0081643
3	0.0071878	0.0070196	0.0076684
4	0.0067061	0.0065728	0.0071506
5	0.0071902	0.0070086	0.0076810
6	0.0064784	0.0063175	0.0068826
7	0.0074391	0.0072982	0.0078961
8	0.0072741	0.0071112	0.0077785
9	0.0087028	0.0085344	0.0091643
10	0.0073034	0.0071957	0.0077402
11	0.0072545	0.0071127	0.0076998
12	0.0073676	0.0071869	0.0078629
13	0.0070782	0.0069520	0.0075517
14	0.0078292	0.0077546	0.0083515
15	0.0088513	0.0087992	0.0093716
16	0.0090042	0.0088870	0.0095468
17	0.0091358	0.0091251	0.0096319
18	0.0075749	0.0074640	0.0080646
19	0.0086534	0.0085857	0.0090404
20	0.0088541	0.0088080	0.0092697
21	0.0092530	0.0092396	0.0097647
22	0.0104660	0.0105487	0.0108801
23	0.0030794	0.0036645	0.0031251

df_total_noth %>%
  group_by(chrom, SUPER) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>% 
  knitr::kable()

`summarise()` has grouped output by 'chrom'. You can override using the
`.groups` argument.

chrom	SUPER	Beagle	Eagle	SHAPEIT
1	AFR	0.0061541	0.0056486	0.0065314
1	AMR	0.0073666	0.0073292	0.0079129
1	EAS	0.0106916	0.0109163	0.0112412
1	EUR	0.0071962	0.0072442	0.0075011
1	SAS	0.0096538	0.0095749	0.0103064
2	AFR	0.0061388	0.0056225	0.0065608
2	AMR	0.0075898	0.0075022	0.0081132
2	EAS	0.0107179	0.0108905	0.0113975
2	EUR	0.0069836	0.0069560	0.0073585
2	SAS	0.0096647	0.0095134	0.0103140
3	AFR	0.0057432	0.0052412	0.0061616
3	AMR	0.0070168	0.0069471	0.0075380
3	EAS	0.0100329	0.0102511	0.0106030
3	EUR	0.0067507	0.0067821	0.0070954
3	SAS	0.0090197	0.0089031	0.0096771
4	AFR	0.0053117	0.0048314	0.0056544
4	AMR	0.0067435	0.0067364	0.0072623
4	EAS	0.0091007	0.0094034	0.0097654
4	EUR	0.0062322	0.0062823	0.0065560
4	SAS	0.0085118	0.0083951	0.0090426
5	AFR	0.0057888	0.0052588	0.0061717
5	AMR	0.0069223	0.0068988	0.0075261
5	EAS	0.0099982	0.0101669	0.0106601
5	EUR	0.0066684	0.0066730	0.0069973
5	SAS	0.0092144	0.0090709	0.0098365
6	AFR	0.0052882	0.0048326	0.0056455
6	AMR	0.0063160	0.0062851	0.0067728
6	EAS	0.0089145	0.0090832	0.0094091
6	EUR	0.0059026	0.0058674	0.0061651
6	SAS	0.0082162	0.0081050	0.0087478
7	AFR	0.0061038	0.0056994	0.0065178
7	AMR	0.0072283	0.0071565	0.0077147
7	EAS	0.0103415	0.0104331	0.0108755
7	EUR	0.0067620	0.0068192	0.0070783
7	SAS	0.0093305	0.0092548	0.0099534
8	AFR	0.0057580	0.0052287	0.0062152
8	AMR	0.0072094	0.0072296	0.0078531
8	EAS	0.0103658	0.0105017	0.0108167
8	EUR	0.0066998	0.0067455	0.0070381
8	SAS	0.0090675	0.0089602	0.0097137
9	AFR	0.0072790	0.0067742	0.0076794
9	AMR	0.0082460	0.0081980	0.0088147
9	EAS	0.0119425	0.0122030	0.0124844
9	EUR	0.0081866	0.0081938	0.0084512
9	SAS	0.0107116	0.0105605	0.0113243
10	AFR	0.0060101	0.0055700	0.0063808
10	AMR	0.0070975	0.0070947	0.0075821
10	EAS	0.0099579	0.0102006	0.0105497
10	EUR	0.0067013	0.0067321	0.0069622
10	SAS	0.0092032	0.0092410	0.0098090
11	AFR	0.0057508	0.0052706	0.0061522
11	AMR	0.0071722	0.0071385	0.0076623
11	EAS	0.0100594	0.0102104	0.0106357
11	EUR	0.0066157	0.0066985	0.0069070
11	SAS	0.0093714	0.0093244	0.0099305
12	AFR	0.0058881	0.0053664	0.0062714
12	AMR	0.0071270	0.0071253	0.0076752
12	EAS	0.0102030	0.0104132	0.0108250
12	EUR	0.0067653	0.0067907	0.0071100
12	SAS	0.0096107	0.0093571	0.0103676
13	AFR	0.0057598	0.0052336	0.0061534
13	AMR	0.0067713	0.0067205	0.0073271
13	EAS	0.0099220	0.0101621	0.0104243
13	EUR	0.0066041	0.0066269	0.0069020
13	SAS	0.0088785	0.0090787	0.0096048
14	AFR	0.0063748	0.0059296	0.0068014
14	AMR	0.0078321	0.0078557	0.0084076
14	EAS	0.0105339	0.0109551	0.0112067
14	EUR	0.0071596	0.0072943	0.0075659
14	SAS	0.0098157	0.0097760	0.0104966
15	AFR	0.0073277	0.0069690	0.0077226
15	AMR	0.0083891	0.0084119	0.0089976
15	EAS	0.0120937	0.0123599	0.0127375
15	EUR	0.0084371	0.0084965	0.0087513
15	SAS	0.0109737	0.0111161	0.0118033
16	AFR	0.0073035	0.0069346	0.0077028
16	AMR	0.0087787	0.0087222	0.0094068
16	EAS	0.0125706	0.0127711	0.0131870
16	EUR	0.0081882	0.0084785	0.0087961
16	SAS	0.0113959	0.0109937	0.0119946
17	AFR	0.0073358	0.0070736	0.0078345
17	AMR	0.0087838	0.0088201	0.0093046
17	EAS	0.0129842	0.0131864	0.0135194
17	EUR	0.0084777	0.0086132	0.0088212
17	SAS	0.0115283	0.0116718	0.0121370
18	AFR	0.0059493	0.0055207	0.0064076
18	AMR	0.0074577	0.0074038	0.0080159
18	EAS	0.0107453	0.0110003	0.0112748
18	EUR	0.0070523	0.0071887	0.0073948
18	SAS	0.0095802	0.0095075	0.0101851
19	AFR	0.0070700	0.0067483	0.0073763
19	AMR	0.0083913	0.0084724	0.0088096
19	EAS	0.0121217	0.0122739	0.0126333
19	EUR	0.0080380	0.0081286	0.0082796
19	SAS	0.0106572	0.0105645	0.0112617
20	AFR	0.0070020	0.0066413	0.0073049
20	AMR	0.0087767	0.0088334	0.0092888
20	EAS	0.0127205	0.0130084	0.0132947
20	EUR	0.0080504	0.0082237	0.0083524
20	SAS	0.0110950	0.0110681	0.0116302
21	AFR	0.0081714	0.0078706	0.0086193
21	AMR	0.0089086	0.0090239	0.0095120
21	EAS	0.0118682	0.0120773	0.0123458
21	EUR	0.0085628	0.0087016	0.0089665
21	SAS	0.0110190	0.0110979	0.0116987
22	AFR	0.0090094	0.0088317	0.0093308
22	AMR	0.0100386	0.0102130	0.0105044
22	EAS	0.0139285	0.0143327	0.0143294
22	EUR	0.0096566	0.0098559	0.0100114
22	SAS	0.0126854	0.0128169	0.0133210
23	AFR	0.0018961	0.0023549	0.0019652
23	AMR	0.0023216	0.0027562	0.0024143
23	EAS	0.0047907	0.0056040	0.0047650
23	EUR	0.0027532	0.0032940	0.0028181
23	SAS	0.0036354	0.0043134	0.0036627

df_total_noth %>%
  group_by(chrom) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>%
  pivot_longer(Beagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  ggplot(aes(x = chrom, y = error_rate, colour = method, shape = method)) +
  geom_point(size=3) +
  theme_bw() +
  xlab("Chromosome") +
  ylab("Error Rate") +
  labs(colour = "Method", shape = "Method") +
  scale_colour_brewer(palette = "Set2") +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5)) +
  scale_x_continuous("Chromosome", labels = as.character(unique(df_total_noth$chrom)), breaks = unique(df_total_noth$chrom))

Past versions of unnamed-chunk-11-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
cb6aa66	Andy Beck	2024-06-06
17d41d5	Andy Beck	2024-05-22
d7d8f5a	Andy Beck	2024-05-22
da672c2	Andy Beck	2024-05-22
4255fdf	Andy Beck	2024-05-21

df_total_noth %>%
  group_by(chrom, SUPER) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>%
  pivot_longer(Beagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  ggplot(aes(x = chrom, y = error_rate, colour = SUPER, shape = method)) +
  geom_point(size=2) +
  theme_bw() +
  ylab("Error Rate") +
  xlab("Chromosome") +
  labs(colour = "Population", shape = "Method") +
  scale_colour_brewer(palette = "Set1") +
  scale_x_continuous("Chromosome", labels = as.character(unique(df_total_noth$chrom)), breaks = unique(df_total_noth$chrom))

`summarise()` has grouped output by 'chrom'. You can override using the
`.groups` argument.

Past versions of unnamed-chunk-11-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
cb6aa66	Andy Beck	2024-06-06
17d41d5	Andy Beck	2024-05-22
d7d8f5a	Andy Beck	2024-05-22
da672c2	Andy Beck	2024-05-22
4255fdf	Andy Beck	2024-05-21

In X, do we see large variation among samples?

df_total %>%
  filter(chrom==23) %>%
  select(Beagle, Eagle, SHAPEIT) %>% summary()

     Beagle              Eagle              SHAPEIT         
 Min.   :0.0004964   Min.   :0.0008379   Min.   :0.0005717  
 1st Qu.:0.0018688   1st Qu.:0.0023121   1st Qu.:0.0019586  
 Median :0.0029121   Median :0.0034861   Median :0.0029834  
 Mean   :0.0030794   Mean   :0.0036645   Mean   :0.0031251  
 3rd Qu.:0.0041509   3rd Qu.:0.0048295   3rd Qu.:0.0041759  
 Max.   :0.0065490   Max.   :0.0074071   Max.   :0.0065881  

What range of values do we observe in the autosomes?

df_total_noth %>%
  select(Beagle, Eagle, SHAPEIT) %>%
  summarize(across(.cols = everything(),
                   .fns = list(
                     mean = ~mean(.x, na.rm =T),
                     sd = ~sd(.x, na.rm = T),
                     min = ~min(.x, na.rm=T),
                     max = ~max(.x, na.rm = T)
                   ),
                   .names = "{.col}_{.fn}") 
            ) %>%
  knitr::kable()

Beagle_mean	Beagle_sd	Beagle_min	Beagle_max	Eagle_mean	Eagle_sd	Eagle_min	Eagle_max	SHAPEIT_mean	SHAPEIT_sd	SHAPEIT_min	SHAPEIT_max
0.0076089	0.0028562	0.0004964	0.0286303	0.0075472	0.0029323	0.0008379	0.0267024	0.0080498	0.002927	0.0005717	0.03858

df_total_noth %>%
  select(chrom, Beagle, Eagle, SHAPEIT) %>%
  group_by(chrom) %>%
  summarize(across(.cols = everything(),
                   .fns = list(
                     mean = ~mean(.x, na.rm =T),
                     sd = ~sd(.x, na.rm = T),
                     min = ~min(.x, na.rm=T),
                     max = ~max(.x, na.rm = T)
                   ),
                   .names = "{.col}_{.fn}") 
            ) %>%
  knitr::kable()

chrom	Beagle_mean	Beagle_sd	Beagle_min	Beagle_max	Eagle_mean	Eagle_sd	Eagle_min	Eagle_max	SHAPEIT_mean	SHAPEIT_sd	SHAPEIT_min	SHAPEIT_max
1	0.0076521	0.0023322	0.0023801	0.0136999	0.0074991	0.0025325	0.0030514	0.0139830	0.0081145	0.0023436	0.0027549	0.0144356
2	0.0076647	0.0023303	0.0029286	0.0133430	0.0074667	0.0025172	0.0023141	0.0139171	0.0081643	0.0023535	0.0040192	0.0141955
3	0.0071878	0.0022068	0.0018160	0.0127320	0.0070196	0.0023905	0.0022519	0.0128360	0.0076684	0.0022175	0.0026375	0.0137675
4	0.0067061	0.0020228	0.0023847	0.0117561	0.0065728	0.0022239	0.0020223	0.0122799	0.0071506	0.0020349	0.0026897	0.0118537
5	0.0071902	0.0022701	0.0027259	0.0126031	0.0070086	0.0024388	0.0019837	0.0127815	0.0076810	0.0023090	0.0033045	0.0130985
6	0.0064784	0.0019903	0.0019080	0.0132438	0.0063175	0.0021561	0.0017240	0.0132704	0.0068826	0.0019991	0.0023244	0.0135365
7	0.0074391	0.0022364	0.0029074	0.0150164	0.0072982	0.0023531	0.0028348	0.0135418	0.0078961	0.0022286	0.0030710	0.0146751
8	0.0072741	0.0023261	0.0028526	0.0135109	0.0071112	0.0025080	0.0026864	0.0137193	0.0077785	0.0023149	0.0035202	0.0149419
9	0.0087028	0.0024156	0.0037646	0.0145061	0.0085344	0.0026200	0.0038298	0.0152881	0.0091643	0.0024335	0.0041561	0.0151824
10	0.0073034	0.0021106	0.0023978	0.0123300	0.0071957	0.0022981	0.0022696	0.0126610	0.0077402	0.0021356	0.0033953	0.0129421
11	0.0072545	0.0023517	0.0024552	0.0132898	0.0071127	0.0025089	0.0021710	0.0137564	0.0076998	0.0023498	0.0029189	0.0138887
12	0.0073676	0.0024640	0.0031297	0.0286303	0.0071869	0.0025879	0.0026982	0.0267024	0.0078629	0.0026569	0.0032827	0.0385800
13	0.0070782	0.0022524	0.0022073	0.0127083	0.0069520	0.0024339	0.0020488	0.0133164	0.0075517	0.0022353	0.0034269	0.0134057
14	0.0078292	0.0023410	0.0023962	0.0159714	0.0077546	0.0025490	0.0022465	0.0166544	0.0083515	0.0024001	0.0031900	0.0157087
15	0.0088513	0.0026191	0.0025277	0.0165449	0.0087992	0.0027724	0.0028078	0.0174337	0.0093716	0.0026636	0.0032533	0.0174043
16	0.0090042	0.0028986	0.0025181	0.0173381	0.0088870	0.0029658	0.0026695	0.0169698	0.0095468	0.0029068	0.0035420	0.0177347
17	0.0091358	0.0029524	0.0030712	0.0173353	0.0091251	0.0030734	0.0028818	0.0176482	0.0096319	0.0029560	0.0035134	0.0174917
18	0.0075749	0.0024421	0.0019858	0.0141914	0.0074640	0.0025959	0.0021564	0.0147436	0.0080646	0.0024261	0.0028701	0.0144952
19	0.0086534	0.0026488	0.0010857	0.0154416	0.0085857	0.0027182	0.0021404	0.0154304	0.0090404	0.0027148	0.0011167	0.0169087
20	0.0088541	0.0029581	0.0029367	0.0205275	0.0088080	0.0031023	0.0029535	0.0219209	0.0092697	0.0029872	0.0033721	0.0209013
21	0.0092530	0.0024265	0.0032546	0.0181752	0.0092396	0.0025532	0.0037141	0.0161322	0.0097647	0.0024139	0.0041352	0.0164855
22	0.0104660	0.0029920	0.0026342	0.0211825	0.0105487	0.0031360	0.0037631	0.0219650	0.0108801	0.0030757	0.0034809	0.0223834
23	0.0030794	0.0013598	0.0004964	0.0065490	0.0036645	0.0014956	0.0008379	0.0074071	0.0031251	0.0013461	0.0005717	0.0065881

Let’s first do a hypothesis test to compare the mean error rates in X versus the autosomes.

# Beagle
autosomes <- df_total_noth %>% filter(chrom < 23) %>% pull(Beagle)
chrX <- df_total_noth %>% filter(chrom == 23) %>% pull(Beagle)
t.test(autosomes, chrX) %>% broom::tidy()

# A tibble: 1 × 10
  estimate estimate1 estimate2 statistic p.value parameter conf.low conf.high
     <dbl>     <dbl>     <dbl>     <dbl>   <dbl>     <dbl>    <dbl>     <dbl>
1  0.00487   0.00795   0.00308      100.       0     1638.  0.00478   0.00497
# ℹ 2 more variables: method <chr>, alternative <chr>

# Eagle
autosomes <- df_total_noth %>% filter(chrom < 23) %>% pull(Eagle)
chrX <- df_total_noth %>% filter(chrom == 23) %>% pull(Eagle)
t.test(autosomes, chrX) %>% broom::tidy()

# A tibble: 1 × 10
  estimate estimate1 estimate2 statistic p.value parameter conf.low conf.high
     <dbl>     <dbl>     <dbl>     <dbl>   <dbl>     <dbl>    <dbl>     <dbl>
1  0.00418   0.00784   0.00366      78.5       0     1591.  0.00407   0.00428
# ℹ 2 more variables: method <chr>, alternative <chr>

# SHAPEIT
autosomes <- df_total_noth %>% filter(chrom < 23) %>% pull(SHAPEIT)
chrX <- df_total_noth %>% filter(chrom == 23) %>% pull(SHAPEIT)
t.test(autosomes, chrX) %>% broom::tidy()

# A tibble: 1 × 10
  estimate estimate1 estimate2 statistic p.value parameter conf.low conf.high
     <dbl>     <dbl>     <dbl>     <dbl>   <dbl>     <dbl>    <dbl>     <dbl>
1  0.00530   0.00842   0.00313      109.       0     1667.  0.00520   0.00539
# ℹ 2 more variables: method <chr>, alternative <chr>

Additionally, I would like to test the null hypothesis that the error rates are the same across chromosomes for each method:

mod_fit <- df_total_noth %>%
  filter(chrom < 23) %>%
  {lmerTest::lmer(Beagle ~ chrom + (1|pair_id), data = .)}

df_anova <- anova(mod_fit) %>% broom::tidy() %>% mutate(method = "Beagle")

Warning in tidy.anova(.): The following column names in ANOVA output were not
recognized or transformed: NumDF, DenDF

mod_fit <- df_total_noth %>%
  filter(chrom < 23) %>%
  {lmerTest::lmer(Eagle ~ chrom + (1|pair_id), data = .)}

df_anova <- bind_rows(df_anova, {anova(mod_fit) %>% broom::tidy() %>% mutate(method = "Eagle")})

Warning in tidy.anova(.): The following column names in ANOVA output were not
recognized or transformed: NumDF, DenDF

mod_fit <- df_total_noth %>%
  filter(chrom < 23) %>%
  {lmerTest::lmer(SHAPEIT ~ chrom + (1|pair_id), data = .)}

df_anova <- bind_rows(df_anova, {anova(mod_fit) %>% broom::tidy() %>% mutate(method = "SHAPEIT")})

Warning in tidy.anova(.): The following column names in ANOVA output were not
recognized or transformed: NumDF, DenDF

df_anova %>%
  knitr::kable()

term	sumsq	meansq	NumDF	DenDF	statistic	p.value	method
chrom	0.0068825	0.0068825	1	12641	4603.281	0	Beagle
chrom	0.0079801	0.0079801	1	12641	5635.171	0	Eagle
chrom	0.0068546	0.0068546	1	12641	4397.972	0	SHAPEIT

For each chromosome, we will test several hypotheses:

1. Are the error rates for Beagle, Eagle, and SHAPEIT the same?
2. If the above does not hold, when we do pairwise comparisons between the methods, are error rates the same?
3. Do error rates differ by population? If so, do above tests separately for each population.

For the first test, I’ll use a linear mixed model with random intercepts for each individual/synthetic diploid. This will also allow me to do contrasts for the pairwise comparisons.

mod_fit <- df_total_noth %>%
  filter(chrom == 1) %>%
  pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  {lmerTest::lmer(error_rate ~ method + (1|pair_id), data = .)}

df_anova <- anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = 1)

df_pairwise <- emmeans::emmeans(mod_fit, ~ method) %>% pairs() %>% broom::tidy() %>% mutate(chrom=1)

for(i in 2:23){
  mod_fit <- df_total_noth %>%
    filter(chrom == i) %>%
    pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
    {lmerTest::lmer(error_rate ~ method + (1|pair_id), data = .)}
  
  df_anova <- df_anova %>% bind_rows({anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = i)})
  df_pairwise <- df_pairwise %>% bind_rows({
    emmeans::emmeans(mod_fit, ~ method) %>% pairs() %>% broom::tidy() %>% mutate(chrom=i)})
}

df_anova %>% knitr::kable()

term	sumsq	meansq	NumDF	DenDF	statistic	p.value	chrom
method	0.0001236	0.0000618	2	1202	656.00360	0	1
method	0.0001556	0.0000778	2	1202	823.78246	0	2
method	0.0001365	0.0000682	2	1202	733.34212	0	3
method	0.0001102	0.0000551	2	1202	559.83128	0	4
method	0.0001456	0.0000728	2	1202	731.43837	0	5
method	0.0001020	0.0000510	2	1202	629.02561	0	6
method	0.0001176	0.0000588	2	1202	576.07381	0	7
method	0.0001457	0.0000729	2	1202	494.42277	0	8
method	0.0001280	0.0000640	2	1202	496.03954	0	9
method	0.0001001	0.0000500	2	1202	462.22172	0	10
method	0.0001130	0.0000565	2	1202	463.45512	0	11
method	0.0001475	0.0000737	2	1202	406.63922	0	12
method	0.0001203	0.0000602	2	1202	340.63110	0	13
method	0.0001273	0.0000637	2	1202	405.14772	0	14
method	0.0001206	0.0000603	2	1202	368.10822	0	15
method	0.0001492	0.0000746	2	1202	299.00932	0	16
method	0.0001009	0.0000505	2	1202	245.86294	0	17
method	0.0001230	0.0000615	2	1202	414.98049	0	18
method	0.0000725	0.0000362	2	1202	181.45836	0	19
method	0.0000779	0.0000389	2	1202	207.08658	0	20
method	0.0001079	0.0000540	2	1202	220.66307	0	21
method	0.0000578	0.0000289	2	1202	96.57538	0	22
method	0.0002118	0.0001059	2	1998	2542.00116	0	23

df_pairwise %>% knitr::kable()

term	contrast	null.value	estimate	std.error	df	statistic	adj.p.value	chrom
method	Beagle - Eagle	0	0.0001530	1.77e-05	1202	8.6488600	0.0000000	1
method	Beagle - SHAPEIT	0	-0.0004624	1.77e-05	1202	-26.1370756	0.0000000	1
method	Eagle - SHAPEIT	0	-0.0006154	1.77e-05	1202	-34.7859356	0.0000000	1
method	Beagle - Eagle	0	0.0001980	1.77e-05	1202	11.1769601	0.0000000	2
method	Beagle - SHAPEIT	0	-0.0004996	1.77e-05	1202	-28.2047198	0.0000000	2
method	Eagle - SHAPEIT	0	-0.0006976	1.77e-05	1202	-39.3816799	0.0000000	2
method	Beagle - Eagle	0	0.0001682	1.76e-05	1202	9.5679959	0.0000000	3
method	Beagle - SHAPEIT	0	-0.0004806	1.76e-05	1202	-27.3306914	0.0000000	3
method	Eagle - SHAPEIT	0	-0.0006488	1.76e-05	1202	-36.8986873	0.0000000	3
method	Beagle - Eagle	0	0.0001333	1.81e-05	1202	7.3721385	0.0000000	4
method	Beagle - SHAPEIT	0	-0.0004445	1.81e-05	1202	-24.5802640	0.0000000	4
method	Eagle - SHAPEIT	0	-0.0005778	1.81e-05	1202	-31.9524025	0.0000000	4
method	Beagle - Eagle	0	0.0001816	1.82e-05	1202	9.9851073	0.0000000	5
method	Beagle - SHAPEIT	0	-0.0004907	1.82e-05	1202	-26.9821360	0.0000000	5
method	Eagle - SHAPEIT	0	-0.0006723	1.82e-05	1202	-36.9672433	0.0000000	5
method	Beagle - Eagle	0	0.0001609	1.64e-05	1202	9.8033434	0.0000000	6
method	Beagle - SHAPEIT	0	-0.0004041	1.64e-05	1202	-24.6188170	0.0000000	6
method	Eagle - SHAPEIT	0	-0.0005651	1.64e-05	1202	-34.4221605	0.0000000	6
method	Beagle - Eagle	0	0.0001409	1.84e-05	1202	7.6532132	0.0000000	7
method	Beagle - SHAPEIT	0	-0.0004569	1.84e-05	1202	-24.8122126	0.0000000	7
method	Eagle - SHAPEIT	0	-0.0005979	1.84e-05	1202	-32.4654258	0.0000000	7
method	Beagle - Eagle	0	0.0001629	2.21e-05	1202	7.3614752	0.0000000	8
method	Beagle - SHAPEIT	0	-0.0005044	2.21e-05	1202	-22.7954906	0.0000000	8
method	Eagle - SHAPEIT	0	-0.0006673	2.21e-05	1202	-30.1569658	0.0000000	8
method	Beagle - Eagle	0	0.0001684	2.07e-05	1202	8.1314831	0.0000000	9
method	Beagle - SHAPEIT	0	-0.0004615	2.07e-05	1202	-22.2870296	0.0000000	9
method	Eagle - SHAPEIT	0	-0.0006299	2.07e-05	1202	-30.4185127	0.0000000	9
method	Beagle - Eagle	0	0.0001077	1.90e-05	1202	5.6775925	0.0000001	10
method	Beagle - SHAPEIT	0	-0.0004368	1.90e-05	1202	-23.0292590	0.0000000	10
method	Eagle - SHAPEIT	0	-0.0005445	1.90e-05	1202	-28.7068515	0.0000000	10
method	Beagle - Eagle	0	0.0001419	2.01e-05	1202	7.0497074	0.0000000	11
method	Beagle - SHAPEIT	0	-0.0004452	2.01e-05	1202	-22.1248811	0.0000000	11
method	Eagle - SHAPEIT	0	-0.0005871	2.01e-05	1202	-29.1745885	0.0000000	11
method	Beagle - Eagle	0	0.0001807	2.45e-05	1202	7.3622141	0.0000000	12
method	Beagle - SHAPEIT	0	-0.0004953	2.45e-05	1202	-20.1790520	0.0000000	12
method	Eagle - SHAPEIT	0	-0.0006760	2.45e-05	1202	-27.5412661	0.0000000	12
method	Beagle - Eagle	0	0.0001262	2.42e-05	1202	5.2086356	0.0000007	13
method	Beagle - SHAPEIT	0	-0.0004735	2.42e-05	1202	-19.5451570	0.0000000	13
method	Eagle - SHAPEIT	0	-0.0005997	2.42e-05	1202	-24.7537925	0.0000000	13
method	Beagle - Eagle	0	0.0000746	2.28e-05	1202	3.2639710	0.0032378	14
method	Beagle - SHAPEIT	0	-0.0005222	2.28e-05	1202	-22.8574295	0.0000000	14
method	Eagle - SHAPEIT	0	-0.0005968	2.28e-05	1202	-26.1214005	0.0000000	14
method	Beagle - Eagle	0	0.0000521	2.33e-05	1202	2.2312906	0.0664182	15
method	Beagle - SHAPEIT	0	-0.0005203	2.33e-05	1202	-22.3029015	0.0000000	15
method	Eagle - SHAPEIT	0	-0.0005724	2.33e-05	1202	-24.5341921	0.0000000	15
method	Beagle - Eagle	0	0.0001172	2.88e-05	1202	4.0717243	0.0001470	16
method	Beagle - SHAPEIT	0	-0.0005426	2.88e-05	1202	-18.8466611	0.0000000	16
method	Eagle - SHAPEIT	0	-0.0006598	2.88e-05	1202	-22.9183854	0.0000000	16
method	Beagle - Eagle	0	0.0000108	2.61e-05	1202	0.4119101	0.9107351	17
method	Beagle - SHAPEIT	0	-0.0004960	2.61e-05	1202	-18.9947521	0.0000000	17
method	Eagle - SHAPEIT	0	-0.0005068	2.61e-05	1202	-19.4066622	0.0000000	17
method	Beagle - Eagle	0	0.0001109	2.22e-05	1202	4.9985018	0.0000020	18
method	Beagle - SHAPEIT	0	-0.0004897	2.22e-05	1202	-22.0717069	0.0000000	18
method	Eagle - SHAPEIT	0	-0.0006006	2.22e-05	1202	-27.0702087	0.0000000	18
method	Beagle - Eagle	0	0.0000677	2.58e-05	1202	2.6289886	0.0235566	19
method	Beagle - SHAPEIT	0	-0.0003870	2.58e-05	1202	-15.0257580	0.0000000	19
method	Eagle - SHAPEIT	0	-0.0004547	2.58e-05	1202	-17.6547467	0.0000000	19
method	Beagle - Eagle	0	0.0000461	2.50e-05	1202	1.8443352	0.1557312	20
method	Beagle - SHAPEIT	0	-0.0004156	2.50e-05	1202	-16.6300028	0.0000000	20
method	Eagle - SHAPEIT	0	-0.0004617	2.50e-05	1202	-18.4743380	0.0000000	20
method	Beagle - Eagle	0	0.0000134	2.85e-05	1202	0.4700150	0.8853898	21
method	Beagle - SHAPEIT	0	-0.0005117	2.85e-05	1202	-17.9536956	0.0000000	21
method	Eagle - SHAPEIT	0	-0.0005251	2.85e-05	1202	-18.4237107	0.0000000	21
method	Beagle - Eagle	0	-0.0000827	3.15e-05	1202	-2.6225872	0.0239835	22
method	Beagle - SHAPEIT	0	-0.0004141	3.15e-05	1202	-13.1309636	0.0000000	22
method	Eagle - SHAPEIT	0	-0.0003314	3.15e-05	1202	-10.5083765	0.0000000	22
method	Beagle - Eagle	0	-0.0005851	9.10e-06	1998	-64.0995718	0.0000000	23
method	Beagle - SHAPEIT	0	-0.0000457	9.10e-06	1998	-5.0047233	0.0000018	23
method	Eagle - SHAPEIT	0	0.0005394	9.10e-06	1998	59.0948484	0.0000000	23

df_pairwise %>%
  filter(adj.p.value > 0.05) %>%
  knitr::kable()

term	contrast	null.value	estimate	std.error	df	statistic	adj.p.value	chrom
method	Beagle - Eagle	0	5.21e-05	2.33e-05	1202	2.2312906	0.0664182	15
method	Beagle - Eagle	0	1.08e-05	2.61e-05	1202	0.4119101	0.9107351	17
method	Beagle - Eagle	0	4.61e-05	2.50e-05	1202	1.8443352	0.1557312	20
method	Beagle - Eagle	0	1.34e-05	2.85e-05	1202	0.4700150	0.8853898	21

Now let’s do these comparisons within each super-population:

mod_fit <- df_total_noth %>%
  filter(chrom == 1) %>%
  pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  {lmerTest::lmer(error_rate ~ method*SUPER + (1|pair_id), data = .)}

df_pop_anova <- anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = 1)

df_pop_pairwise <- emmeans::emmeans(mod_fit, ~ method | SUPER) %>% pairs() %>% broom::tidy() %>% mutate(chrom=1)
df_pop_pop <- emmeans::emmeans(mod_fit, ~ SUPER | method) %>% pairs() %>% broom::tidy() %>% mutate(chrom = 1)

for(i in 2:23){
  mod_fit <- df_total_noth %>%
    filter(chrom == i) %>%
    pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
    {lmerTest::lmer(error_rate ~ method*SUPER + (1|pair_id), data = .)}
  
  df_pop_anova <- df_pop_anova %>% bind_rows({anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = i)})
  df_pop_pairwise <- df_pop_pairwise %>% bind_rows({
    emmeans::emmeans(mod_fit, ~ method | SUPER) %>% pairs() %>% broom::tidy() %>% mutate(chrom=i)})
  df_pop_pop <- df_pop_pop %>% bind_rows({
    emmeans::emmeans(mod_fit, ~ SUPER | method) %>% pairs() %>% broom::tidy() %>% mutate(chrom = i)})
}

df_pop_anova %>% knitr::kable()

term	sumsq	meansq	NumDF	DenDF	statistic	p.value	chrom
method	0.0000970	0.0000485	2	1194.0000	684.993557	0	1
SUPER	0.0000403	0.0000101	4	597.0000	142.135219	0	1
method:SUPER	0.0000287	0.0000036	8	1194.0000	50.640353	0	1
method	0.0001270	0.0000635	2	1194.0000	834.414662	0	2
SUPER	0.0000456	0.0000114	4	597.0000	149.664197	0	2
method:SUPER	0.0000226	0.0000028	8	1194.0000	37.178475	0	2
method	0.0001072	0.0000536	2	1194.0000	751.821151	0	3
SUPER	0.0000396	0.0000099	4	597.0000	138.951458	0	3
method:SUPER	0.0000267	0.0000033	8	1194.0000	46.847777	0	3
method	0.0000892	0.0000446	2	1194.0000	577.945676	0	4
SUPER	0.0000448	0.0000112	4	597.0000	145.126286	0	4
method:SUPER	0.0000261	0.0000033	8	1194.0000	42.270907	0	4
method	0.0001184	0.0000592	2	1194.0000	756.839178	0	5
SUPER	0.0000413	0.0000103	4	597.0000	131.905501	0	5
method:SUPER	0.0000263	0.0000033	8	1194.0000	42.028809	0	5
method	0.0000792	0.0000396	2	1194.0000	609.514893	0	6
SUPER	0.0000322	0.0000081	4	597.0000	124.060370	0	6
method:SUPER	0.0000200	0.0000025	8	1194.0000	38.422997	0	6
method	0.0000952	0.0000476	2	1194.0000	541.823084	0	7
SUPER	0.0000468	0.0000117	4	596.9999	133.235429	0	7
method:SUPER	0.0000178	0.0000022	8	1194.0000	25.282506	0	7
method	0.0001089	0.0000545	2	1194.0000	448.195973	0	8
SUPER	0.0000662	0.0000166	4	597.0000	136.218054	0	8
method:SUPER	0.0000321	0.0000040	8	1194.0000	32.986322	0	8
method	0.0000978	0.0000489	2	1194.0000	467.435725	0	9
SUPER	0.0000558	0.0000139	4	597.0000	133.284760	0	9
method:SUPER	0.0000302	0.0000038	8	1194.0000	36.062684	0	9
method	0.0000800	0.0000400	2	1194.0000	451.764809	0	10
SUPER	0.0000498	0.0000124	4	596.9999	140.515094	0	10
method:SUPER	0.0000244	0.0000030	8	1194.0000	34.400393	0	10
method	0.0000880	0.0000440	2	1194.0000	435.589782	0	11
SUPER	0.0000532	0.0000133	4	596.9999	131.798942	0	11
method:SUPER	0.0000259	0.0000032	8	1194.0000	32.068560	0	11
method	0.0001238	0.0000619	2	1194.0001	398.164349	0	12
SUPER	0.0000701	0.0000175	4	596.9996	112.723771	0	12
method:SUPER	0.0000323	0.0000040	8	1194.0001	25.975115	0	12
method	0.0000906	0.0000453	2	1194.0000	305.359265	0	13
SUPER	0.0000761	0.0000190	4	597.0000	128.286830	0	13
method:SUPER	0.0000352	0.0000044	8	1194.0000	29.645340	0	13
method	0.0001040	0.0000520	2	1194.0000	395.555364	0	14
SUPER	0.0000617	0.0000154	4	597.0000	117.352113	0	14
method:SUPER	0.0000318	0.0000040	8	1194.0000	30.269096	0	14
method	0.0001049	0.0000524	2	1194.0000	361.313934	0	15
SUPER	0.0000679	0.0000170	4	597.0000	116.984755	0	15
method:SUPER	0.0000236	0.0000029	8	1194.0000	20.318197	0	15
method	0.0001297	0.0000649	2	1194.0000	283.660734	0	16
SUPER	0.0001029	0.0000257	4	596.9999	112.494890	0	16
method:SUPER	0.0000269	0.0000034	8	1194.0000	14.684099	0	16
method	0.0000805	0.0000403	2	1194.0000	208.716218	0	17
SUPER	0.0000959	0.0000240	4	597.0000	124.243178	0	17
method:SUPER	0.0000164	0.0000021	8	1194.0000	10.644324	0	17
method	0.0000938	0.0000469	2	1194.0000	372.147639	0	18
SUPER	0.0000713	0.0000178	4	597.0000	141.355742	0	18
method:SUPER	0.0000276	0.0000034	8	1194.0000	27.352646	0	18
method	0.0000639	0.0000320	2	1194.0000	172.053799	0	19
SUPER	0.0000894	0.0000223	4	597.0000	120.274053	0	19
method:SUPER	0.0000182	0.0000023	8	1194.0000	12.225247	0	19
method	0.0000661	0.0000330	2	1194.0000	193.320266	0	20
SUPER	0.0000866	0.0000217	4	597.0000	126.782913	0	20
method:SUPER	0.0000220	0.0000027	8	1194.0000	16.080003	0	20
method	0.0000882	0.0000441	2	1194.0000	190.791026	0	21
SUPER	0.0000665	0.0000166	4	597.0000	71.906930	0	21
method:SUPER	0.0000180	0.0000023	8	1194.0000	9.744354	0	21
method	0.0000520	0.0000260	2	1194.0000	90.499127	0	22
SUPER	0.0000934	0.0000234	4	597.0000	81.308769	0	22
method:SUPER	0.0000168	0.0000021	8	1194.0000	7.295923	0	22
method	0.0002118	0.0001059	2	1990.0000	3255.331545	0	23
SUPER	0.0000458	0.0000114	4	994.9999	351.584878	0	23
method:SUPER	0.0000185	0.0000023	8	1990.0000	71.084254	0	23

df_pop_pairwise %>% knitr::kable()

SUPER	term	contrast	null.value	estimate	std.error	df	statistic	adj.p.value	chrom
AFR	method	Beagle - Eagle	0	0.0005055	2.65e-05	1194	19.0440527	0.0000000	1
AFR	method	Beagle - SHAPEIT	0	-0.0003773	2.65e-05	1194	-14.2151091	0.0000000	1
AFR	method	Eagle - SHAPEIT	0	-0.0008828	2.65e-05	1194	-33.2591618	0.0000000	1
AMR	method	Beagle - Eagle	0	0.0000373	3.22e-05	1194	1.1614326	0.4765626	1
AMR	method	Beagle - SHAPEIT	0	-0.0005463	3.22e-05	1194	-16.9923411	0.0000000	1
AMR	method	Eagle - SHAPEIT	0	-0.0005837	3.22e-05	1194	-18.1537736	0.0000000	1
EAS	method	Beagle - Eagle	0	-0.0002248	4.44e-05	1194	-5.0678399	0.0000014	1
EAS	method	Beagle - SHAPEIT	0	-0.0005496	4.44e-05	1194	-12.3933265	0.0000000	1
EAS	method	Eagle - SHAPEIT	0	-0.0003249	4.44e-05	1194	-7.3254866	0.0000000	1
EUR	method	Beagle - Eagle	0	-0.0000480	3.64e-05	1194	-1.3200650	0.3842343	1
EUR	method	Beagle - SHAPEIT	0	-0.0003049	3.64e-05	1194	-8.3808704	0.0000000	1
EUR	method	Eagle - SHAPEIT	0	-0.0002569	3.64e-05	1194	-7.0608053	0.0000000	1
SAS	method	Beagle - Eagle	0	0.0000789	4.08e-05	1194	1.9338974	0.1296453	1
SAS	method	Beagle - SHAPEIT	0	-0.0006526	4.08e-05	1194	-15.9880567	0.0000000	1
SAS	method	Eagle - SHAPEIT	0	-0.0007315	4.08e-05	1194	-17.9219541	0.0000000	1
AFR	method	Beagle - Eagle	0	0.0005163	2.75e-05	1194	18.7620053	0.0000000	2
AFR	method	Beagle - SHAPEIT	0	-0.0004220	2.75e-05	1194	-15.3352301	0.0000000	2
AFR	method	Eagle - SHAPEIT	0	-0.0009383	2.75e-05	1194	-34.0972354	0.0000000	2
AMR	method	Beagle - Eagle	0	0.0000877	3.33e-05	1194	2.6305211	0.0234572	2
AMR	method	Beagle - SHAPEIT	0	-0.0005233	3.33e-05	1194	-15.7005189	0.0000000	2
AMR	method	Eagle - SHAPEIT	0	-0.0006110	3.33e-05	1194	-18.3310400	0.0000000	2
EAS	method	Beagle - Eagle	0	-0.0001726	4.60e-05	1194	-3.7529039	0.0005369	2
EAS	method	Beagle - SHAPEIT	0	-0.0006795	4.60e-05	1194	-14.7788721	0.0000000	2
EAS	method	Eagle - SHAPEIT	0	-0.0005070	4.60e-05	1194	-11.0259682	0.0000000	2
EUR	method	Beagle - Eagle	0	0.0000276	3.77e-05	1194	0.7308715	0.7452005	2
EUR	method	Beagle - SHAPEIT	0	-0.0003749	3.77e-05	1194	-9.9396659	0.0000000	2
EUR	method	Eagle - SHAPEIT	0	-0.0004025	3.77e-05	1194	-10.6705374	0.0000000	2
SAS	method	Beagle - Eagle	0	0.0001513	4.23e-05	1194	3.5759958	0.0010564	2
SAS	method	Beagle - SHAPEIT	0	-0.0006492	4.23e-05	1194	-15.3418032	0.0000000	2
SAS	method	Eagle - SHAPEIT	0	-0.0008006	4.23e-05	1194	-18.9177990	0.0000000	2
AFR	method	Beagle - Eagle	0	0.0005019	2.66e-05	1194	18.8439898	0.0000000	3
AFR	method	Beagle - SHAPEIT	0	-0.0004184	2.66e-05	1194	-15.7075197	0.0000000	3
AFR	method	Eagle - SHAPEIT	0	-0.0009203	2.66e-05	1194	-34.5515095	0.0000000	3
AMR	method	Beagle - Eagle	0	0.0000697	3.23e-05	1194	2.1604475	0.0785432	3
AMR	method	Beagle - SHAPEIT	0	-0.0005212	3.23e-05	1194	-16.1544877	0.0000000	3
AMR	method	Eagle - SHAPEIT	0	-0.0005909	3.23e-05	1194	-18.3149352	0.0000000	3
EAS	method	Beagle - Eagle	0	-0.0002182	4.45e-05	1194	-4.9020919	0.0000032	3
EAS	method	Beagle - SHAPEIT	0	-0.0005701	4.45e-05	1194	-12.8090854	0.0000000	3
EAS	method	Eagle - SHAPEIT	0	-0.0003519	4.45e-05	1194	-7.9069935	0.0000000	3
EUR	method	Beagle - Eagle	0	-0.0000314	3.65e-05	1194	-0.8600196	0.6656372	3
EUR	method	Beagle - SHAPEIT	0	-0.0003447	3.65e-05	1194	-9.4407418	0.0000000	3
EUR	method	Eagle - SHAPEIT	0	-0.0003133	3.65e-05	1194	-8.5807222	0.0000000	3
SAS	method	Beagle - Eagle	0	0.0001166	4.10e-05	1194	2.8459360	0.0125104	3
SAS	method	Beagle - SHAPEIT	0	-0.0006574	4.10e-05	1194	-16.0492012	0.0000000	3
SAS	method	Eagle - SHAPEIT	0	-0.0007740	4.10e-05	1194	-18.8951372	0.0000000	3
AFR	method	Beagle - Eagle	0	0.0004803	2.77e-05	1194	17.3264765	0.0000000	4
AFR	method	Beagle - SHAPEIT	0	-0.0003427	2.77e-05	1194	-12.3642277	0.0000000	4
AFR	method	Eagle - SHAPEIT	0	-0.0008230	2.77e-05	1194	-29.6907042	0.0000000	4
AMR	method	Beagle - Eagle	0	0.0000071	3.36e-05	1194	0.2106180	0.9758425	4
AMR	method	Beagle - SHAPEIT	0	-0.0005188	3.36e-05	1194	-15.4513339	0.0000000	4
AMR	method	Eagle - SHAPEIT	0	-0.0005258	3.36e-05	1194	-15.6619519	0.0000000	4
EAS	method	Beagle - Eagle	0	-0.0003027	4.63e-05	1194	-6.5366803	0.0000000	4
EAS	method	Beagle - SHAPEIT	0	-0.0006647	4.63e-05	1194	-14.3531006	0.0000000	4
EAS	method	Eagle - SHAPEIT	0	-0.0003620	4.63e-05	1194	-7.8164202	0.0000000	4
EUR	method	Beagle - Eagle	0	-0.0000502	3.80e-05	1194	-1.3208221	0.3838147	4
EUR	method	Beagle - SHAPEIT	0	-0.0003238	3.80e-05	1194	-8.5229063	0.0000000	4
EUR	method	Eagle - SHAPEIT	0	-0.0002736	3.80e-05	1194	-7.2020843	0.0000000	4
SAS	method	Beagle - Eagle	0	0.0001167	4.26e-05	1194	2.7371383	0.0172855	4
SAS	method	Beagle - SHAPEIT	0	-0.0005308	4.26e-05	1194	-12.4524035	0.0000000	4
SAS	method	Eagle - SHAPEIT	0	-0.0006474	4.26e-05	1194	-15.1895418	0.0000000	4
AFR	method	Beagle - Eagle	0	0.0005300	2.79e-05	1194	19.0005097	0.0000000	5
AFR	method	Beagle - SHAPEIT	0	-0.0003829	2.79e-05	1194	-13.7265817	0.0000000	5
AFR	method	Eagle - SHAPEIT	0	-0.0009129	2.79e-05	1194	-32.7270914	0.0000000	5
AMR	method	Beagle - Eagle	0	0.0000235	3.38e-05	1194	0.6966320	0.7655009	5
AMR	method	Beagle - SHAPEIT	0	-0.0006038	3.38e-05	1194	-17.8693578	0.0000000	5
AMR	method	Eagle - SHAPEIT	0	-0.0006273	3.38e-05	1194	-18.5659898	0.0000000	5
EAS	method	Beagle - Eagle	0	-0.0001687	4.66e-05	1194	-3.6196228	0.0008965	5
EAS	method	Beagle - SHAPEIT	0	-0.0006619	4.66e-05	1194	-14.2010224	0.0000000	5
EAS	method	Eagle - SHAPEIT	0	-0.0004932	4.66e-05	1194	-10.5813996	0.0000000	5
EUR	method	Beagle - Eagle	0	-0.0000046	3.82e-05	1194	-0.1198941	0.9921065	5
EUR	method	Beagle - SHAPEIT	0	-0.0003289	3.82e-05	1194	-8.6024373	0.0000000	5
EUR	method	Eagle - SHAPEIT	0	-0.0003243	3.82e-05	1194	-8.4825432	0.0000000	5
SAS	method	Beagle - Eagle	0	0.0001435	4.29e-05	1194	3.3457221	0.0024368	5
SAS	method	Beagle - SHAPEIT	0	-0.0006222	4.29e-05	1194	-14.5038132	0.0000000	5
SAS	method	Eagle - SHAPEIT	0	-0.0007657	4.29e-05	1194	-17.8495353	0.0000000	5
AFR	method	Beagle - Eagle	0	0.0004556	2.54e-05	1194	17.9232098	0.0000000	6
AFR	method	Beagle - SHAPEIT	0	-0.0003573	2.54e-05	1194	-14.0579172	0.0000000	6
AFR	method	Eagle - SHAPEIT	0	-0.0008129	2.54e-05	1194	-31.9811270	0.0000000	6
AMR	method	Beagle - Eagle	0	0.0000309	3.08e-05	1194	1.0047598	0.5739814	6
AMR	method	Beagle - SHAPEIT	0	-0.0004568	3.08e-05	1194	-14.8351085	0.0000000	6
AMR	method	Eagle - SHAPEIT	0	-0.0004877	3.08e-05	1194	-15.8398683	0.0000000	6
EAS	method	Beagle - Eagle	0	-0.0001687	4.25e-05	1194	-3.9722441	0.0002226	6
EAS	method	Beagle - SHAPEIT	0	-0.0004946	4.25e-05	1194	-11.6451918	0.0000000	6
EAS	method	Eagle - SHAPEIT	0	-0.0003259	4.25e-05	1194	-7.6729477	0.0000000	6
EUR	method	Beagle - Eagle	0	0.0000351	3.48e-05	1194	1.0086359	0.5715297	6
EUR	method	Beagle - SHAPEIT	0	-0.0002625	3.48e-05	1194	-7.5354147	0.0000000	6
EUR	method	Eagle - SHAPEIT	0	-0.0002977	3.48e-05	1194	-8.5440506	0.0000000	6
SAS	method	Beagle - Eagle	0	0.0001112	3.91e-05	1194	2.8449610	0.0125474	6
SAS	method	Beagle - SHAPEIT	0	-0.0005316	3.91e-05	1194	-13.5994183	0.0000000	6
SAS	method	Eagle - SHAPEIT	0	-0.0006428	3.91e-05	1194	-16.4443792	0.0000000	6
AFR	method	Beagle - Eagle	0	0.0004044	2.96e-05	1194	13.6777630	0.0000000	7
AFR	method	Beagle - SHAPEIT	0	-0.0004139	2.96e-05	1194	-13.9984462	0.0000000	7
AFR	method	Eagle - SHAPEIT	0	-0.0008184	2.96e-05	1194	-27.6762091	0.0000000	7
AMR	method	Beagle - Eagle	0	0.0000718	3.58e-05	1194	2.0038332	0.1116978	7
AMR	method	Beagle - SHAPEIT	0	-0.0004864	3.58e-05	1194	-13.5804758	0.0000000	7
AMR	method	Eagle - SHAPEIT	0	-0.0005582	3.58e-05	1194	-15.5843090	0.0000000	7
EAS	method	Beagle - Eagle	0	-0.0000917	4.94e-05	1194	-1.8552389	0.1523649	7
EAS	method	Beagle - SHAPEIT	0	-0.0005340	4.94e-05	1194	-10.8082895	0.0000000	7
EAS	method	Eagle - SHAPEIT	0	-0.0004423	4.94e-05	1194	-8.9530505	0.0000000	7
EUR	method	Beagle - Eagle	0	-0.0000572	4.05e-05	1194	-1.4112475	0.3353662	7
EUR	method	Beagle - SHAPEIT	0	-0.0003163	4.05e-05	1194	-7.8036290	0.0000000	7
EUR	method	Eagle - SHAPEIT	0	-0.0002591	4.05e-05	1194	-6.3923814	0.0000000	7
SAS	method	Beagle - Eagle	0	0.0000757	4.55e-05	1194	1.6652420	0.2190879	7
SAS	method	Beagle - SHAPEIT	0	-0.0006228	4.55e-05	1194	-13.6977318	0.0000000	7
SAS	method	Eagle - SHAPEIT	0	-0.0006986	4.55e-05	1194	-15.3629738	0.0000000	7
AFR	method	Beagle - Eagle	0	0.0005292	3.48e-05	1194	15.2191879	0.0000000	8
AFR	method	Beagle - SHAPEIT	0	-0.0004572	3.48e-05	1194	-13.1492904	0.0000000	8
AFR	method	Eagle - SHAPEIT	0	-0.0009865	3.48e-05	1194	-28.3684784	0.0000000	8
AMR	method	Beagle - Eagle	0	-0.0000202	4.21e-05	1194	-0.4797532	0.8808918	8
AMR	method	Beagle - SHAPEIT	0	-0.0006436	4.21e-05	1194	-15.2815689	0.0000000	8
AMR	method	Eagle - SHAPEIT	0	-0.0006234	4.21e-05	1194	-14.8018156	0.0000000	8
EAS	method	Beagle - Eagle	0	-0.0001358	5.81e-05	1194	-2.3378961	0.0511116	8
EAS	method	Beagle - SHAPEIT	0	-0.0004508	5.81e-05	1194	-7.7595044	0.0000000	8
EAS	method	Eagle - SHAPEIT	0	-0.0003150	5.81e-05	1194	-5.4216082	0.0000002	8
EUR	method	Beagle - Eagle	0	-0.0000456	4.77e-05	1194	-0.9576612	0.6038381	8
EUR	method	Beagle - SHAPEIT	0	-0.0003383	4.77e-05	1194	-7.0978298	0.0000000	8
EUR	method	Eagle - SHAPEIT	0	-0.0002926	4.77e-05	1194	-6.1401686	0.0000000	8
SAS	method	Beagle - Eagle	0	0.0001073	5.35e-05	1194	2.0074336	0.1108289	8
SAS	method	Beagle - SHAPEIT	0	-0.0006462	5.35e-05	1194	-12.0846881	0.0000000	8
SAS	method	Eagle - SHAPEIT	0	-0.0007535	5.35e-05	1194	-14.0921217	0.0000000	8
AFR	method	Beagle - Eagle	0	0.0005048	3.23e-05	1194	15.6450576	0.0000000	9
AFR	method	Beagle - SHAPEIT	0	-0.0004004	3.23e-05	1194	-12.4092070	0.0000000	9
AFR	method	Eagle - SHAPEIT	0	-0.0009052	3.23e-05	1194	-28.0542646	0.0000000	9
AMR	method	Beagle - Eagle	0	0.0000480	3.91e-05	1194	1.2283880	0.4365983	9
AMR	method	Beagle - SHAPEIT	0	-0.0005687	3.91e-05	1194	-14.5519496	0.0000000	9
AMR	method	Eagle - SHAPEIT	0	-0.0006168	3.91e-05	1194	-15.7803376	0.0000000	9
EAS	method	Beagle - Eagle	0	-0.0002605	5.39e-05	1194	-4.8323648	0.0000046	9
EAS	method	Beagle - SHAPEIT	0	-0.0005420	5.39e-05	1194	-10.0524216	0.0000000	9
EAS	method	Eagle - SHAPEIT	0	-0.0002814	5.39e-05	1194	-5.2200568	0.0000006	9
EUR	method	Beagle - Eagle	0	-0.0000072	4.42e-05	1194	-0.1623164	0.9855803	9
EUR	method	Beagle - SHAPEIT	0	-0.0002646	4.42e-05	1194	-5.9827613	0.0000000	9
EUR	method	Eagle - SHAPEIT	0	-0.0002574	4.42e-05	1194	-5.8204448	0.0000000	9
SAS	method	Beagle - Eagle	0	0.0001511	4.96e-05	1194	3.0445454	0.0067259	9
SAS	method	Beagle - SHAPEIT	0	-0.0006127	4.96e-05	1194	-12.3486181	0.0000000	9
SAS	method	Eagle - SHAPEIT	0	-0.0007638	4.96e-05	1194	-15.3931635	0.0000000	9
AFR	method	Beagle - Eagle	0	0.0004400	2.97e-05	1194	14.8217605	0.0000000	10
AFR	method	Beagle - SHAPEIT	0	-0.0003707	2.97e-05	1194	-12.4868312	0.0000000	10
AFR	method	Eagle - SHAPEIT	0	-0.0008108	2.97e-05	1194	-27.3085918	0.0000000	10
AMR	method	Beagle - Eagle	0	0.0000027	3.60e-05	1194	0.0763676	0.9967899	10
AMR	method	Beagle - SHAPEIT	0	-0.0004847	3.60e-05	1194	-13.4772797	0.0000000	10
AMR	method	Eagle - SHAPEIT	0	-0.0004874	3.60e-05	1194	-13.5536472	0.0000000	10
EAS	method	Beagle - Eagle	0	-0.0002428	4.96e-05	1194	-4.8937123	0.0000034	10
EAS	method	Beagle - SHAPEIT	0	-0.0005918	4.96e-05	1194	-11.9304773	0.0000000	10
EAS	method	Eagle - SHAPEIT	0	-0.0003491	4.96e-05	1194	-7.0367650	0.0000000	10
EUR	method	Beagle - Eagle	0	-0.0000309	4.07e-05	1194	-0.7583770	0.7286062	10
EUR	method	Beagle - SHAPEIT	0	-0.0002610	4.07e-05	1194	-6.4133877	0.0000000	10
EUR	method	Eagle - SHAPEIT	0	-0.0002301	4.07e-05	1194	-5.6550107	0.0000001	10
SAS	method	Beagle - Eagle	0	-0.0000379	4.57e-05	1194	-0.8296017	0.6846975	10
SAS	method	Beagle - SHAPEIT	0	-0.0006058	4.57e-05	1194	-13.2696823	0.0000000	10
SAS	method	Eagle - SHAPEIT	0	-0.0005679	4.57e-05	1194	-12.4400806	0.0000000	10
AFR	method	Beagle - Eagle	0	0.0004802	3.17e-05	1194	15.1488380	0.0000000	11
AFR	method	Beagle - SHAPEIT	0	-0.0004014	3.17e-05	1194	-12.6630091	0.0000000	11
AFR	method	Eagle - SHAPEIT	0	-0.0008817	3.17e-05	1194	-27.8118471	0.0000000	11
AMR	method	Beagle - Eagle	0	0.0000337	3.84e-05	1194	0.8768243	0.6550521	11
AMR	method	Beagle - SHAPEIT	0	-0.0004901	3.84e-05	1194	-12.7643833	0.0000000	11
AMR	method	Eagle - SHAPEIT	0	-0.0005238	3.84e-05	1194	-13.6412075	0.0000000	11
EAS	method	Beagle - Eagle	0	-0.0001510	5.30e-05	1194	-2.8508519	0.0123255	11
EAS	method	Beagle - SHAPEIT	0	-0.0005763	5.30e-05	1194	-10.8796391	0.0000000	11
EAS	method	Eagle - SHAPEIT	0	-0.0004253	5.30e-05	1194	-8.0287872	0.0000000	11
EUR	method	Beagle - Eagle	0	-0.0000828	4.34e-05	1194	-1.9064647	0.1372569	11
EUR	method	Beagle - SHAPEIT	0	-0.0002914	4.34e-05	1194	-6.7057425	0.0000000	11
EUR	method	Eagle - SHAPEIT	0	-0.0002085	4.34e-05	1194	-4.7992778	0.0000054	11
SAS	method	Beagle - Eagle	0	0.0000470	4.87e-05	1194	0.9641536	0.5997178	11
SAS	method	Beagle - SHAPEIT	0	-0.0005590	4.87e-05	1194	-11.4674726	0.0000000	11
SAS	method	Eagle - SHAPEIT	0	-0.0006060	4.87e-05	1194	-12.4316263	0.0000000	11
AFR	method	Beagle - Eagle	0	0.0005216	3.93e-05	1194	13.2622619	0.0000000	12
AFR	method	Beagle - SHAPEIT	0	-0.0003833	3.93e-05	1194	-9.7459948	0.0000000	12
AFR	method	Eagle - SHAPEIT	0	-0.0009050	3.93e-05	1194	-23.0082566	0.0000000	12
AMR	method	Beagle - Eagle	0	0.0000017	4.76e-05	1194	0.0347542	0.9993343	12
AMR	method	Beagle - SHAPEIT	0	-0.0005482	4.76e-05	1194	-11.5070928	0.0000000	12
AMR	method	Eagle - SHAPEIT	0	-0.0005499	4.76e-05	1194	-11.5418470	0.0000000	12
EAS	method	Beagle - Eagle	0	-0.0002102	6.57e-05	1194	-3.1985743	0.0040464	12
EAS	method	Beagle - SHAPEIT	0	-0.0006219	6.57e-05	1194	-9.4639273	0.0000000	12
EAS	method	Eagle - SHAPEIT	0	-0.0004117	6.57e-05	1194	-6.2653530	0.0000000	12
EUR	method	Beagle - Eagle	0	-0.0000254	5.39e-05	1194	-0.4711667	0.8848616	12
EUR	method	Beagle - SHAPEIT	0	-0.0003447	5.39e-05	1194	-6.3939818	0.0000000	12
EUR	method	Eagle - SHAPEIT	0	-0.0003193	5.39e-05	1194	-5.9228152	0.0000000	12
SAS	method	Beagle - Eagle	0	0.0002536	6.05e-05	1194	4.1928331	0.0000877	12
SAS	method	Beagle - SHAPEIT	0	-0.0007569	6.05e-05	1194	-12.5137184	0.0000000	12
SAS	method	Eagle - SHAPEIT	0	-0.0010105	6.05e-05	1194	-16.7065515	0.0000000	12
AFR	method	Beagle - Eagle	0	0.0005261	3.84e-05	1194	13.6934555	0.0000000	13
AFR	method	Beagle - SHAPEIT	0	-0.0003936	3.84e-05	1194	-10.2447170	0.0000000	13
AFR	method	Eagle - SHAPEIT	0	-0.0009197	3.84e-05	1194	-23.9381725	0.0000000	13
AMR	method	Beagle - Eagle	0	0.0000508	4.65e-05	1194	1.0915984	0.5194596	13
AMR	method	Beagle - SHAPEIT	0	-0.0005557	4.65e-05	1194	-11.9413517	0.0000000	13
AMR	method	Eagle - SHAPEIT	0	-0.0006065	4.65e-05	1194	-13.0329500	0.0000000	13
EAS	method	Beagle - Eagle	0	-0.0002402	6.42e-05	1194	-3.7413941	0.0005616	13
EAS	method	Beagle - SHAPEIT	0	-0.0005023	6.42e-05	1194	-7.8252429	0.0000000	13
EAS	method	Eagle - SHAPEIT	0	-0.0002622	6.42e-05	1194	-4.0838488	0.0001397	13
EUR	method	Beagle - Eagle	0	-0.0000228	5.27e-05	1194	-0.4331872	0.9017594	13
EUR	method	Beagle - SHAPEIT	0	-0.0002979	5.27e-05	1194	-5.6572024	0.0000001	13
EUR	method	Eagle - SHAPEIT	0	-0.0002751	5.27e-05	1194	-5.2240152	0.0000006	13
SAS	method	Beagle - Eagle	0	-0.0002002	5.91e-05	1194	-3.3883083	0.0020959	13
SAS	method	Beagle - SHAPEIT	0	-0.0007263	5.91e-05	1194	-12.2937546	0.0000000	13
SAS	method	Eagle - SHAPEIT	0	-0.0005262	5.91e-05	1194	-8.9054463	0.0000000	13
AFR	method	Beagle - Eagle	0	0.0004452	3.62e-05	1194	12.3085578	0.0000000	14
AFR	method	Beagle - SHAPEIT	0	-0.0004266	3.62e-05	1194	-11.7920322	0.0000000	14
AFR	method	Eagle - SHAPEIT	0	-0.0008718	3.62e-05	1194	-24.1005900	0.0000000	14
AMR	method	Beagle - Eagle	0	-0.0000236	4.38e-05	1194	-0.5377136	0.8527486	14
AMR	method	Beagle - SHAPEIT	0	-0.0005755	4.38e-05	1194	-13.1343977	0.0000000	14
AMR	method	Eagle - SHAPEIT	0	-0.0005519	4.38e-05	1194	-12.5966841	0.0000000	14
EAS	method	Beagle - Eagle	0	-0.0004212	6.04e-05	1194	-6.9683875	0.0000000	14
EAS	method	Beagle - SHAPEIT	0	-0.0006728	6.04e-05	1194	-11.1314465	0.0000000	14
EAS	method	Eagle - SHAPEIT	0	-0.0002516	6.04e-05	1194	-4.1630590	0.0000997	14
EUR	method	Beagle - Eagle	0	-0.0001347	4.96e-05	1194	-2.7177888	0.0182858	14
EUR	method	Beagle - SHAPEIT	0	-0.0004064	4.96e-05	1194	-8.1964235	0.0000000	14
EUR	method	Eagle - SHAPEIT	0	-0.0002716	4.96e-05	1194	-5.4786347	0.0000002	14
SAS	method	Beagle - Eagle	0	0.0000396	5.56e-05	1194	0.7124864	0.7561536	14
SAS	method	Beagle - SHAPEIT	0	-0.0006810	5.56e-05	1194	-12.2420022	0.0000000	14
SAS	method	Eagle - SHAPEIT	0	-0.0007206	5.56e-05	1194	-12.9544886	0.0000000	14
AFR	method	Beagle - Eagle	0	0.0003587	3.80e-05	1194	9.4386505	0.0000000	15
AFR	method	Beagle - SHAPEIT	0	-0.0003949	3.80e-05	1194	-10.3903120	0.0000000	15
AFR	method	Eagle - SHAPEIT	0	-0.0007536	3.80e-05	1194	-19.8289624	0.0000000	15
AMR	method	Beagle - Eagle	0	-0.0000228	4.60e-05	1194	-0.4962488	0.8731169	15
AMR	method	Beagle - SHAPEIT	0	-0.0006085	4.60e-05	1194	-13.2192618	0.0000000	15
AMR	method	Eagle - SHAPEIT	0	-0.0005857	4.60e-05	1194	-12.7230130	0.0000000	15
EAS	method	Beagle - Eagle	0	-0.0002662	6.35e-05	1194	-4.1924257	0.0000878	15
EAS	method	Beagle - SHAPEIT	0	-0.0006438	6.35e-05	1194	-10.1394519	0.0000000	15
EAS	method	Eagle - SHAPEIT	0	-0.0003776	6.35e-05	1194	-5.9470262	0.0000000	15
EUR	method	Beagle - Eagle	0	-0.0000594	5.21e-05	1194	-1.1409907	0.4890059	15
EUR	method	Beagle - SHAPEIT	0	-0.0003142	5.21e-05	1194	-6.0314706	0.0000000	15
EUR	method	Eagle - SHAPEIT	0	-0.0002547	5.21e-05	1194	-4.8904799	0.0000034	15
SAS	method	Beagle - Eagle	0	-0.0001424	5.84e-05	1194	-2.4374077	0.0396042	15
SAS	method	Beagle - SHAPEIT	0	-0.0008296	5.84e-05	1194	-14.1949264	0.0000000	15
SAS	method	Eagle - SHAPEIT	0	-0.0006871	5.84e-05	1194	-11.7575187	0.0000000	15
AFR	method	Beagle - Eagle	0	0.0003689	4.77e-05	1194	7.7338629	0.0000000	16
AFR	method	Beagle - SHAPEIT	0	-0.0003993	4.77e-05	1194	-8.3715322	0.0000000	16
AFR	method	Eagle - SHAPEIT	0	-0.0007682	4.77e-05	1194	-16.1053950	0.0000000	16
AMR	method	Beagle - Eagle	0	0.0000565	5.78e-05	1194	0.9779683	0.5909538	16
AMR	method	Beagle - SHAPEIT	0	-0.0006281	5.78e-05	1194	-10.8712620	0.0000000	16
AMR	method	Eagle - SHAPEIT	0	-0.0006846	5.78e-05	1194	-11.8492303	0.0000000	16
EAS	method	Beagle - Eagle	0	-0.0002005	7.97e-05	1194	-2.5156145	0.0321812	16
EAS	method	Beagle - SHAPEIT	0	-0.0006164	7.97e-05	1194	-7.7342443	0.0000000	16
EAS	method	Eagle - SHAPEIT	0	-0.0004159	7.97e-05	1194	-5.2186298	0.0000006	16
EUR	method	Beagle - Eagle	0	-0.0002904	6.54e-05	1194	-4.4419836	0.0000290	16
EUR	method	Beagle - SHAPEIT	0	-0.0006080	6.54e-05	1194	-9.2998373	0.0000000	16
EUR	method	Eagle - SHAPEIT	0	-0.0003176	6.54e-05	1194	-4.8578538	0.0000040	16
SAS	method	Beagle - Eagle	0	0.0004022	7.33e-05	1194	5.4832923	0.0000002	16
SAS	method	Beagle - SHAPEIT	0	-0.0005987	7.33e-05	1194	-8.1627773	0.0000000	16
SAS	method	Eagle - SHAPEIT	0	-0.0010009	7.33e-05	1194	-13.6460695	0.0000000	16
AFR	method	Beagle - Eagle	0	0.0002622	4.38e-05	1194	5.9858512	0.0000000	17
AFR	method	Beagle - SHAPEIT	0	-0.0004987	4.38e-05	1194	-11.3826610	0.0000000	17
AFR	method	Eagle - SHAPEIT	0	-0.0007609	4.38e-05	1194	-17.3685122	0.0000000	17
AMR	method	Beagle - Eagle	0	-0.0000364	5.31e-05	1194	-0.6852430	0.7721556	17
AMR	method	Beagle - SHAPEIT	0	-0.0005208	5.31e-05	1194	-9.8149434	0.0000000	17
AMR	method	Eagle - SHAPEIT	0	-0.0004845	5.31e-05	1194	-9.1297004	0.0000000	17
EAS	method	Beagle - Eagle	0	-0.0002022	7.32e-05	1194	-2.7617166	0.0160847	17
EAS	method	Beagle - SHAPEIT	0	-0.0005352	7.32e-05	1194	-7.3110209	0.0000000	17
EAS	method	Eagle - SHAPEIT	0	-0.0003330	7.32e-05	1194	-4.5493043	0.0000177	17
EUR	method	Beagle - Eagle	0	-0.0001355	6.00e-05	1194	-2.2565365	0.0624910	17
EUR	method	Beagle - SHAPEIT	0	-0.0003435	6.00e-05	1194	-5.7210562	0.0000000	17
EUR	method	Eagle - SHAPEIT	0	-0.0002080	6.00e-05	1194	-3.4645197	0.0015934	17
SAS	method	Beagle - Eagle	0	-0.0001435	6.74e-05	1194	-2.1304709	0.0841853	17
SAS	method	Beagle - SHAPEIT	0	-0.0006087	6.74e-05	1194	-9.0352654	0.0000000	17
SAS	method	Eagle - SHAPEIT	0	-0.0004652	6.74e-05	1194	-6.9047945	0.0000000	17
AFR	method	Beagle - Eagle	0	0.0004286	3.54e-05	1194	12.1029163	0.0000000	18
AFR	method	Beagle - SHAPEIT	0	-0.0004583	3.54e-05	1194	-12.9413121	0.0000000	18
AFR	method	Eagle - SHAPEIT	0	-0.0008869	3.54e-05	1194	-25.0442284	0.0000000	18
AMR	method	Beagle - Eagle	0	0.0000538	4.29e-05	1194	1.2552844	0.4209309	18
AMR	method	Beagle - SHAPEIT	0	-0.0005582	4.29e-05	1194	-13.0135443	0.0000000	18
AMR	method	Eagle - SHAPEIT	0	-0.0006121	4.29e-05	1194	-14.2688287	0.0000000	18
EAS	method	Beagle - Eagle	0	-0.0002549	5.92e-05	1194	-4.3080744	0.0000529	18
EAS	method	Beagle - SHAPEIT	0	-0.0005295	5.92e-05	1194	-8.9482588	0.0000000	18
EAS	method	Eagle - SHAPEIT	0	-0.0002746	5.92e-05	1194	-4.6401844	0.0000115	18
EUR	method	Beagle - Eagle	0	-0.0001363	4.85e-05	1194	-2.8088141	0.0139881	18
EUR	method	Beagle - SHAPEIT	0	-0.0003425	4.85e-05	1194	-7.0553912	0.0000000	18
EUR	method	Eagle - SHAPEIT	0	-0.0002061	4.85e-05	1194	-4.2465772	0.0000694	18
SAS	method	Beagle - Eagle	0	0.0000726	5.45e-05	1194	1.3331711	0.3770016	18
SAS	method	Beagle - SHAPEIT	0	-0.0006050	5.45e-05	1194	-11.1083313	0.0000000	18
SAS	method	Eagle - SHAPEIT	0	-0.0006776	5.45e-05	1194	-12.4415024	0.0000000	18
AFR	method	Beagle - Eagle	0	0.0003216	4.30e-05	1194	7.4813169	0.0000000	19
AFR	method	Beagle - SHAPEIT	0	-0.0003063	4.30e-05	1194	-7.1249908	0.0000000	19
AFR	method	Eagle - SHAPEIT	0	-0.0006280	4.30e-05	1194	-14.6063077	0.0000000	19
AMR	method	Beagle - Eagle	0	-0.0000811	5.21e-05	1194	-1.5577378	0.2645574	19
AMR	method	Beagle - SHAPEIT	0	-0.0004183	5.21e-05	1194	-8.0328288	0.0000000	19
AMR	method	Eagle - SHAPEIT	0	-0.0003372	5.21e-05	1194	-6.4750909	0.0000000	19
EAS	method	Beagle - Eagle	0	-0.0001522	7.18e-05	1194	-2.1189795	0.0864328	19
EAS	method	Beagle - SHAPEIT	0	-0.0005116	7.18e-05	1194	-7.1215054	0.0000000	19
EAS	method	Eagle - SHAPEIT	0	-0.0003593	7.18e-05	1194	-5.0025259	0.0000019	19
EUR	method	Beagle - Eagle	0	-0.0000906	5.89e-05	1194	-1.5378709	0.2735718	19
EUR	method	Beagle - SHAPEIT	0	-0.0002416	5.89e-05	1194	-4.1009873	0.0001299	19
EUR	method	Eagle - SHAPEIT	0	-0.0001510	5.89e-05	1194	-2.5631163	0.0282837	19
SAS	method	Beagle - Eagle	0	0.0000927	6.61e-05	1194	1.4019229	0.3402032	19
SAS	method	Beagle - SHAPEIT	0	-0.0006045	6.61e-05	1194	-9.1442675	0.0000000	19
SAS	method	Eagle - SHAPEIT	0	-0.0006972	6.61e-05	1194	-10.5461904	0.0000000	19
AFR	method	Beagle - Eagle	0	0.0003607	4.12e-05	1194	8.7486537	0.0000000	20
AFR	method	Beagle - SHAPEIT	0	-0.0003029	4.12e-05	1194	-7.3462005	0.0000000	20
AFR	method	Eagle - SHAPEIT	0	-0.0006636	4.12e-05	1194	-16.0948542	0.0000000	20
AMR	method	Beagle - Eagle	0	-0.0000567	4.99e-05	1194	-1.1358979	0.4921217	20
AMR	method	Beagle - SHAPEIT	0	-0.0005121	4.99e-05	1194	-10.2540553	0.0000000	20
AMR	method	Eagle - SHAPEIT	0	-0.0004554	4.99e-05	1194	-9.1181574	0.0000000	20
EAS	method	Beagle - Eagle	0	-0.0002879	6.89e-05	1194	-4.1788964	0.0000931	20
EAS	method	Beagle - SHAPEIT	0	-0.0005742	6.89e-05	1194	-8.3355057	0.0000000	20
EAS	method	Eagle - SHAPEIT	0	-0.0002863	6.89e-05	1194	-4.1566093	0.0001025	20
EUR	method	Beagle - Eagle	0	-0.0001733	5.65e-05	1194	-3.0673045	0.0062486	20
EUR	method	Beagle - SHAPEIT	0	-0.0003020	5.65e-05	1194	-5.3445971	0.0000003	20
EUR	method	Eagle - SHAPEIT	0	-0.0001287	5.65e-05	1194	-2.2772926	0.0594055	20
SAS	method	Beagle - Eagle	0	0.0000269	6.34e-05	1194	0.4249621	0.9052721	20
SAS	method	Beagle - SHAPEIT	0	-0.0005352	6.34e-05	1194	-8.4418609	0.0000000	20
SAS	method	Eagle - SHAPEIT	0	-0.0005622	6.34e-05	1194	-8.8668230	0.0000000	20
AFR	method	Beagle - Eagle	0	0.0003008	4.79e-05	1194	6.2726141	0.0000000	21
AFR	method	Beagle - SHAPEIT	0	-0.0004479	4.79e-05	1194	-9.3411600	0.0000000	21
AFR	method	Eagle - SHAPEIT	0	-0.0007487	4.79e-05	1194	-15.6137740	0.0000000	21
AMR	method	Beagle - Eagle	0	-0.0001152	5.81e-05	1194	-1.9843647	0.1164881	21
AMR	method	Beagle - SHAPEIT	0	-0.0006034	5.81e-05	1194	-10.3886910	0.0000000	21
AMR	method	Eagle - SHAPEIT	0	-0.0004881	5.81e-05	1194	-8.4043262	0.0000000	21
EAS	method	Beagle - Eagle	0	-0.0002090	8.01e-05	1194	-2.6088978	0.0249208	21
EAS	method	Beagle - SHAPEIT	0	-0.0004776	8.01e-05	1194	-5.9608976	0.0000000	21
EAS	method	Eagle - SHAPEIT	0	-0.0002685	8.01e-05	1194	-3.3519998	0.0023836	21
EUR	method	Beagle - Eagle	0	-0.0001388	6.57e-05	1194	-2.1114952	0.0879222	21
EUR	method	Beagle - SHAPEIT	0	-0.0004037	6.57e-05	1194	-6.1423595	0.0000000	21
EUR	method	Eagle - SHAPEIT	0	-0.0002649	6.57e-05	1194	-4.0308643	0.0001745	21
SAS	method	Beagle - Eagle	0	-0.0000789	7.37e-05	1194	-1.0696380	0.5331493	21
SAS	method	Beagle - SHAPEIT	0	-0.0006798	7.37e-05	1194	-9.2191316	0.0000000	21
SAS	method	Eagle - SHAPEIT	0	-0.0006009	7.37e-05	1194	-8.1494936	0.0000000	21
AFR	method	Beagle - Eagle	0	0.0001776	5.35e-05	1194	3.3221526	0.0026468	22
AFR	method	Beagle - SHAPEIT	0	-0.0003215	5.35e-05	1194	-6.0125758	0.0000000	22
AFR	method	Eagle - SHAPEIT	0	-0.0004991	5.35e-05	1194	-9.3347284	0.0000000	22
AMR	method	Beagle - Eagle	0	-0.0001744	6.48e-05	1194	-2.6923316	0.0196794	22
AMR	method	Beagle - SHAPEIT	0	-0.0004658	6.48e-05	1194	-7.1925821	0.0000000	22
AMR	method	Eagle - SHAPEIT	0	-0.0002914	6.48e-05	1194	-4.5002504	0.0000222	22
EAS	method	Beagle - Eagle	0	-0.0004043	8.93e-05	1194	-4.5254701	0.0000197	22
EAS	method	Beagle - SHAPEIT	0	-0.0004010	8.93e-05	1194	-4.4883624	0.0000234	22
EAS	method	Eagle - SHAPEIT	0	0.0000033	8.93e-05	1194	0.0371077	0.9992411	22
EUR	method	Beagle - Eagle	0	-0.0001993	7.33e-05	1194	-2.7191826	0.0182121	22
EUR	method	Beagle - SHAPEIT	0	-0.0003548	7.33e-05	1194	-4.8410279	0.0000044	22
EUR	method	Eagle - SHAPEIT	0	-0.0001555	7.33e-05	1194	-2.1218453	0.0858678	22
SAS	method	Beagle - Eagle	0	-0.0001315	8.22e-05	1194	-1.5988523	0.2465055	22
SAS	method	Beagle - SHAPEIT	0	-0.0006356	8.22e-05	1194	-7.7299990	0.0000000	22
SAS	method	Eagle - SHAPEIT	0	-0.0005041	8.22e-05	1194	-6.1311467	0.0000000	22
AFR	method	Beagle - Eagle	0	-0.0004588	1.80e-05	1990	-25.4372255	0.0000000	23
AFR	method	Beagle - SHAPEIT	0	-0.0000692	1.80e-05	1990	-3.8350570	0.0003805	23
AFR	method	Eagle - SHAPEIT	0	0.0003896	1.80e-05	1990	21.6021685	0.0000000	23
AMR	method	Beagle - Eagle	0	-0.0004346	1.80e-05	1990	-24.0941650	0.0000000	23
AMR	method	Beagle - SHAPEIT	0	-0.0000927	1.80e-05	1990	-5.1416197	0.0000009	23
AMR	method	Eagle - SHAPEIT	0	0.0003418	1.80e-05	1990	18.9525452	0.0000000	23
EAS	method	Beagle - Eagle	0	-0.0008134	1.80e-05	1990	-45.0949894	0.0000000	23
EAS	method	Beagle - SHAPEIT	0	0.0000256	1.80e-05	1990	1.4204075	0.3305162	23
EAS	method	Eagle - SHAPEIT	0	0.0008390	1.80e-05	1990	46.5153968	0.0000000	23
EUR	method	Beagle - Eagle	0	-0.0005408	1.80e-05	1990	-29.9828894	0.0000000	23
EUR	method	Beagle - SHAPEIT	0	-0.0000649	1.80e-05	1990	-3.5966972	0.0009624	23
EUR	method	Eagle - SHAPEIT	0	0.0004759	1.80e-05	1990	26.3861922	0.0000000	23
SAS	method	Beagle - Eagle	0	-0.0006780	1.80e-05	1990	-37.5903655	0.0000000	23
SAS	method	Beagle - SHAPEIT	0	-0.0000273	1.80e-05	1990	-1.5111478	0.2858440	23
SAS	method	Eagle - SHAPEIT	0	0.0006508	1.80e-05	1990	36.0792178	0.0000000	23

df_pop_pop %>% knitr::kable()

method	term	contrast	null.value	estimate	std.error	df	statistic	adj.p.value	chrom
Beagle	SUPER	AFR - AMR	0	-0.0012125	0.0001918	616.1882	-6.3226634	0.0000000	1
Beagle	SUPER	AFR - EAS	0	-0.0045375	0.0002377	616.1882	-19.0863327	0.0000000	1
Beagle	SUPER	AFR - EUR	0	-0.0010421	0.0002071	616.1882	-5.0308144	0.0000064	1
Beagle	SUPER	AFR - SAS	0	-0.0034997	0.0002240	616.1882	-15.6273412	0.0000000	1
Beagle	SUPER	AMR - EAS	0	-0.0033250	0.0002520	616.1882	-13.1968292	0.0000000	1
Beagle	SUPER	AMR - EUR	0	0.0001704	0.0002233	616.1882	0.7630794	0.9410205	1
Beagle	SUPER	AMR - SAS	0	-0.0022873	0.0002390	616.1882	-9.5704702	0.0000000	1
Beagle	SUPER	EAS - EUR	0	0.0034954	0.0002638	616.1882	13.2481109	0.0000000	1
Beagle	SUPER	EAS - SAS	0	0.0010377	0.0002772	616.1882	3.7431667	0.0018528	1
Beagle	SUPER	EUR - SAS	0	-0.0024577	0.0002515	616.1882	-9.7723339	0.0000000	1
Eagle	SUPER	AFR - AMR	0	-0.0016806	0.0001918	616.1882	-8.7639580	0.0000000	1
Eagle	SUPER	AFR - EAS	0	-0.0052678	0.0002377	616.1882	-22.1580917	0.0000000	1
Eagle	SUPER	AFR - EUR	0	-0.0015956	0.0002071	616.1882	-7.7030756	0.0000000	1
Eagle	SUPER	AFR - SAS	0	-0.0039263	0.0002240	616.1882	-17.5320761	0.0000000	1
Eagle	SUPER	AMR - EAS	0	-0.0035871	0.0002520	616.1882	-14.2371048	0.0000000	1
Eagle	SUPER	AMR - EUR	0	0.0000850	0.0002233	616.1882	0.3808090	0.9955331	1
Eagle	SUPER	AMR - SAS	0	-0.0022457	0.0002390	616.1882	-9.3964212	0.0000000	1
Eagle	SUPER	EAS - EUR	0	0.0036721	0.0002638	616.1882	13.9179639	0.0000000	1
Eagle	SUPER	EAS - SAS	0	0.0013414	0.0002772	616.1882	4.8386172	0.0000163	1
Eagle	SUPER	EUR - SAS	0	-0.0023307	0.0002515	616.1882	-9.2674955	0.0000000	1
SHAPEIT	SUPER	AFR - AMR	0	-0.0013815	0.0001918	616.1882	-7.2039711	0.0000000	1
SHAPEIT	SUPER	AFR - EAS	0	-0.0047098	0.0002377	616.1882	-19.8111881	0.0000000	1
SHAPEIT	SUPER	AFR - EUR	0	-0.0009697	0.0002071	616.1882	-4.6811806	0.0000345	1
SHAPEIT	SUPER	AFR - SAS	0	-0.0037750	0.0002240	616.1882	-16.8565374	0.0000000	1
SHAPEIT	SUPER	AMR - EAS	0	-0.0033283	0.0002520	616.1882	-13.2099938	0.0000000	1
SHAPEIT	SUPER	AMR - EUR	0	0.0004118	0.0002233	616.1882	1.8441927	0.3491025	1
SHAPEIT	SUPER	AMR - SAS	0	-0.0023935	0.0002390	616.1882	-10.0151392	0.0000000	1
SHAPEIT	SUPER	EAS - EUR	0	0.0037402	0.0002638	616.1882	14.1757339	0.0000000	1
SHAPEIT	SUPER	EAS - SAS	0	0.0009348	0.0002772	616.1882	3.3718037	0.0070774	1
SHAPEIT	SUPER	EUR - SAS	0	-0.0028054	0.0002515	616.1882	-11.1548852	0.0000000	1
Beagle	SUPER	AFR - AMR	0	-0.0014510	0.0001893	618.2141	-7.6661287	0.0000000	2
Beagle	SUPER	AFR - EAS	0	-0.0045791	0.0002346	618.2141	-19.5149909	0.0000000	2
Beagle	SUPER	AFR - EUR	0	-0.0008447	0.0002044	618.2141	-4.1317571	0.0003933	2
Beagle	SUPER	AFR - SAS	0	-0.0035259	0.0002210	618.2141	-15.9513954	0.0000000	2
Beagle	SUPER	AMR - EAS	0	-0.0031281	0.0002487	618.2141	-12.5787557	0.0000000	2
Beagle	SUPER	AMR - EUR	0	0.0006063	0.0002204	618.2141	2.7506861	0.0480162	2
Beagle	SUPER	AMR - SAS	0	-0.0020749	0.0002359	618.2141	-8.7961269	0.0000000	2
Beagle	SUPER	EAS - EUR	0	0.0037344	0.0002604	618.2141	14.3401901	0.0000000	2
Beagle	SUPER	EAS - SAS	0	0.0010532	0.0002736	618.2141	3.8489790	0.0012325	2
Beagle	SUPER	EUR - SAS	0	-0.0026812	0.0002482	618.2141	-10.8013964	0.0000000	2
Eagle	SUPER	AFR - AMR	0	-0.0018796	0.0001893	618.2141	-9.9307186	0.0000000	2
Eagle	SUPER	AFR - EAS	0	-0.0052680	0.0002346	618.2141	-22.4507941	0.0000000	2
Eagle	SUPER	AFR - EUR	0	-0.0013335	0.0002044	618.2141	-6.5223458	0.0000000	2
Eagle	SUPER	AFR - SAS	0	-0.0038909	0.0002210	618.2141	-17.6026197	0.0000000	2
Eagle	SUPER	AMR - EAS	0	-0.0033883	0.0002487	618.2141	-13.6252422	0.0000000	2
Eagle	SUPER	AMR - EUR	0	0.0005462	0.0002204	618.2141	2.4779423	0.0969742	2
Eagle	SUPER	AMR - SAS	0	-0.0020112	0.0002359	618.2141	-8.5263112	0.0000000	2
Eagle	SUPER	EAS - EUR	0	0.0039345	0.0002604	618.2141	15.1086773	0.0000000	2
Eagle	SUPER	EAS - SAS	0	0.0013771	0.0002736	618.2141	5.0326298	0.0000063	2
Eagle	SUPER	EUR - SAS	0	-0.0025574	0.0002482	618.2141	-10.3028069	0.0000000	2
SHAPEIT	SUPER	AFR - AMR	0	-0.0015523	0.0001893	618.2141	-8.2014905	0.0000000	2
SHAPEIT	SUPER	AFR - EAS	0	-0.0048366	0.0002346	618.2141	-20.6124634	0.0000000	2
SHAPEIT	SUPER	AFR - EUR	0	-0.0007976	0.0002044	618.2141	-3.9013075	0.0010036	2
SHAPEIT	SUPER	AFR - SAS	0	-0.0037531	0.0002210	618.2141	-16.9793542	0.0000000	2
SHAPEIT	SUPER	AMR - EAS	0	-0.0032843	0.0002487	618.2141	-13.2068142	0.0000000	2
SHAPEIT	SUPER	AMR - EUR	0	0.0007547	0.0002204	618.2141	3.4241741	0.0059079	2
SHAPEIT	SUPER	AMR - SAS	0	-0.0022008	0.0002359	618.2141	-9.3298123	0.0000000	2
SHAPEIT	SUPER	EAS - EUR	0	0.0040390	0.0002604	618.2141	15.5099899	0.0000000	2
SHAPEIT	SUPER	EAS - SAS	0	0.0010835	0.0002736	618.2141	3.9597004	0.0007954	2
SHAPEIT	SUPER	EUR - SAS	0	-0.0029555	0.0002482	618.2141	-11.9065845	0.0000000	2
Beagle	SUPER	AFR - AMR	0	-0.0012736	0.0001824	618.4175	-6.9842973	0.0000000	3
Beagle	SUPER	AFR - EAS	0	-0.0042897	0.0002261	618.4175	-18.9757873	0.0000000	3
Beagle	SUPER	AFR - EUR	0	-0.0010075	0.0001970	618.4175	-5.1150992	0.0000042	3
Beagle	SUPER	AFR - SAS	0	-0.0032765	0.0002130	618.4175	-15.3859277	0.0000000	3
Beagle	SUPER	AMR - EAS	0	-0.0030161	0.0002396	618.4175	-12.5889395	0.0000000	3
Beagle	SUPER	AMR - EUR	0	0.0002661	0.0002124	618.4175	1.2530659	0.7200460	3
Beagle	SUPER	AMR - SAS	0	-0.0020029	0.0002273	618.4175	-8.8133525	0.0000000	3
Beagle	SUPER	EAS - EUR	0	0.0032822	0.0002509	618.4175	13.0823331	0.0000000	3
Beagle	SUPER	EAS - SAS	0	0.0010132	0.0002636	618.4175	3.8433848	0.0012597	3
Beagle	SUPER	EUR - SAS	0	-0.0022690	0.0002391	618.4175	-9.4879388	0.0000000	3
Eagle	SUPER	AFR - AMR	0	-0.0017058	0.0001824	618.4175	-9.3546293	0.0000000	3
Eagle	SUPER	AFR - EAS	0	-0.0050098	0.0002261	618.4175	-22.1612288	0.0000000	3
Eagle	SUPER	AFR - EUR	0	-0.0015409	0.0001970	618.4175	-7.8228288	0.0000000	3
Eagle	SUPER	AFR - SAS	0	-0.0036619	0.0002130	618.4175	-17.1955558	0.0000000	3
Eagle	SUPER	AMR - EAS	0	-0.0033040	0.0002396	618.4175	-13.7904928	0.0000000	3
Eagle	SUPER	AMR - EUR	0	0.0001650	0.0002124	618.4175	0.7769585	0.9372165	3
Eagle	SUPER	AMR - SAS	0	-0.0019560	0.0002273	618.4175	-8.6071232	0.0000000	3
Eagle	SUPER	EAS - EUR	0	0.0034690	0.0002509	618.4175	13.8267740	0.0000000	3
Eagle	SUPER	EAS - SAS	0	0.0013479	0.0002636	618.4175	5.1131469	0.0000042	3
Eagle	SUPER	EUR - SAS	0	-0.0021210	0.0002391	618.4175	-8.8691961	0.0000000	3
SHAPEIT	SUPER	AFR - AMR	0	-0.0013764	0.0001824	618.4175	-7.5481042	0.0000000	3
SHAPEIT	SUPER	AFR - EAS	0	-0.0044414	0.0002261	618.4175	-19.6467338	0.0000000	3
SHAPEIT	SUPER	AFR - EUR	0	-0.0009338	0.0001970	618.4175	-4.7407509	0.0000260	3
SHAPEIT	SUPER	AFR - SAS	0	-0.0035155	0.0002130	618.4175	-16.5081940	0.0000000	3
SHAPEIT	SUPER	AMR - EAS	0	-0.0030650	0.0002396	618.4175	-12.7928942	0.0000000	3
SHAPEIT	SUPER	AMR - EUR	0	0.0004426	0.0002124	618.4175	2.0844555	0.2280753	3
SHAPEIT	SUPER	AMR - SAS	0	-0.0021391	0.0002273	618.4175	-9.4125857	0.0000000	3
SHAPEIT	SUPER	EAS - EUR	0	0.0035076	0.0002509	618.4175	13.9807848	0.0000000	3
SHAPEIT	SUPER	EAS - SAS	0	0.0009259	0.0002636	618.4175	3.5121715	0.0043348	3
SHAPEIT	SUPER	EUR - SAS	0	-0.0025817	0.0002391	618.4175	-10.7956267	0.0000000	3
Beagle	SUPER	AFR - AMR	0	-0.0014318	0.0001666	624.9824	-8.5965559	0.0000000	4
Beagle	SUPER	AFR - EAS	0	-0.0037890	0.0002065	624.9824	-18.3502878	0.0000000	4
Beagle	SUPER	AFR - EUR	0	-0.0009205	0.0001799	624.9824	-5.1164543	0.0000041	4
Beagle	SUPER	AFR - SAS	0	-0.0032001	0.0001945	624.9824	-16.4523674	0.0000000	4
Beagle	SUPER	AMR - EAS	0	-0.0023572	0.0002188	624.9824	-10.7716189	0.0000000	4
Beagle	SUPER	AMR - EUR	0	0.0005113	0.0001940	624.9824	2.6363058	0.0651550	4
Beagle	SUPER	AMR - SAS	0	-0.0017683	0.0002076	624.9824	-8.5189904	0.0000000	4
Beagle	SUPER	EAS - EUR	0	0.0028685	0.0002292	624.9824	12.5176632	0.0000000	4
Beagle	SUPER	EAS - SAS	0	0.0005889	0.0002408	624.9824	2.4455429	0.1047865	4
Beagle	SUPER	EUR - SAS	0	-0.0022796	0.0002184	624.9824	-10.4364704	0.0000000	4
Eagle	SUPER	AFR - AMR	0	-0.0019050	0.0001666	624.9824	-11.4375177	0.0000000	4
Eagle	SUPER	AFR - EAS	0	-0.0045719	0.0002065	624.9824	-22.1423035	0.0000000	4
Eagle	SUPER	AFR - EUR	0	-0.0014509	0.0001799	624.9824	-8.0648147	0.0000000	4
Eagle	SUPER	AFR - SAS	0	-0.0035637	0.0001945	624.9824	-18.3216285	0.0000000	4
Eagle	SUPER	AMR - EAS	0	-0.0026670	0.0002188	624.9824	-12.1873065	0.0000000	4
Eagle	SUPER	AMR - EUR	0	0.0004541	0.0001940	624.9824	2.3411432	0.1334060	4
Eagle	SUPER	AMR - SAS	0	-0.0016587	0.0002076	624.9824	-7.9910055	0.0000000	4
Eagle	SUPER	EAS - EUR	0	0.0031210	0.0002292	624.9824	13.6197417	0.0000000	4
Eagle	SUPER	EAS - SAS	0	0.0010082	0.0002408	624.9824	4.1872818	0.0003111	4
Eagle	SUPER	EUR - SAS	0	-0.0021128	0.0002184	624.9824	-9.6726375	0.0000000	4
SHAPEIT	SUPER	AFR - AMR	0	-0.0016079	0.0001666	624.9824	-9.6535308	0.0000000	4
SHAPEIT	SUPER	AFR - EAS	0	-0.0041110	0.0002065	624.9824	-19.9097927	0.0000000	4
SHAPEIT	SUPER	AFR - EUR	0	-0.0009016	0.0001799	624.9824	-5.0112483	0.0000070	4
SHAPEIT	SUPER	AFR - SAS	0	-0.0033882	0.0001945	624.9824	-17.4191854	0.0000000	4
SHAPEIT	SUPER	AMR - EAS	0	-0.0025031	0.0002188	624.9824	-11.4386233	0.0000000	4
SHAPEIT	SUPER	AMR - EUR	0	0.0007063	0.0001940	624.9824	3.6415483	0.0027082	4
SHAPEIT	SUPER	AMR - SAS	0	-0.0017803	0.0002076	624.9824	-8.5768384	0.0000000	4
SHAPEIT	SUPER	EAS - EUR	0	0.0032094	0.0002292	624.9824	14.0054502	0.0000000	4
SHAPEIT	SUPER	EAS - SAS	0	0.0007228	0.0002408	624.9824	3.0018544	0.0232890	4
SHAPEIT	SUPER	EUR - SAS	0	-0.0024866	0.0002184	624.9824	-11.3840583	0.0000000	4
Beagle	SUPER	AFR - AMR	0	-0.0011335	0.0001901	618.6204	-5.9628756	0.0000000	5
Beagle	SUPER	AFR - EAS	0	-0.0042093	0.0002357	618.6204	-17.8622579	0.0000000	5
Beagle	SUPER	AFR - EUR	0	-0.0008796	0.0002053	618.6204	-4.2837826	0.0002062	5
Beagle	SUPER	AFR - SAS	0	-0.0034256	0.0002220	618.6204	-15.4310327	0.0000000	5
Beagle	SUPER	AMR - EAS	0	-0.0030759	0.0002498	618.6204	-12.3156806	0.0000000	5
Beagle	SUPER	AMR - EUR	0	0.0002539	0.0002214	618.6204	1.1470363	0.7813251	5
Beagle	SUPER	AMR - SAS	0	-0.0022921	0.0002369	618.6204	-9.6752120	0.0000000	5
Beagle	SUPER	EAS - EUR	0	0.0033298	0.0002615	618.6204	12.7316428	0.0000000	5
Beagle	SUPER	EAS - SAS	0	0.0007838	0.0002748	618.6204	2.8520784	0.0361675	5
Beagle	SUPER	EUR - SAS	0	-0.0025460	0.0002493	618.6204	-10.2128077	0.0000000	5
Eagle	SUPER	AFR - AMR	0	-0.0016400	0.0001901	618.6204	-8.6273259	0.0000000	5
Eagle	SUPER	AFR - EAS	0	-0.0049081	0.0002357	618.6204	-20.8273037	0.0000000	5
Eagle	SUPER	AFR - EUR	0	-0.0014142	0.0002053	618.6204	-6.8874783	0.0000000	5
Eagle	SUPER	AFR - SAS	0	-0.0038121	0.0002220	618.6204	-17.1721184	0.0000000	5
Eagle	SUPER	AMR - EAS	0	-0.0032681	0.0002498	618.6204	-13.0854173	0.0000000	5
Eagle	SUPER	AMR - EUR	0	0.0002258	0.0002214	618.6204	1.0199953	0.8461585	5
Eagle	SUPER	AMR - SAS	0	-0.0021721	0.0002369	618.6204	-9.1687524	0.0000000	5
Eagle	SUPER	EAS - EUR	0	0.0034939	0.0002615	618.6204	13.3591717	0.0000000	5
Eagle	SUPER	EAS - SAS	0	0.0010960	0.0002748	618.6204	3.9882156	0.0007091	5
Eagle	SUPER	EUR - SAS	0	-0.0023979	0.0002493	618.6204	-9.6187154	0.0000000	5
SHAPEIT	SUPER	AFR - AMR	0	-0.0013544	0.0001901	618.6204	-7.1248035	0.0000000	5
SHAPEIT	SUPER	AFR - EAS	0	-0.0044883	0.0002357	618.6204	-19.0460952	0.0000000	5
SHAPEIT	SUPER	AFR - EUR	0	-0.0008256	0.0002053	618.6204	-4.0207336	0.0006216	5
SHAPEIT	SUPER	AFR - SAS	0	-0.0036648	0.0002220	618.6204	-16.5087887	0.0000000	5
SHAPEIT	SUPER	AMR - EAS	0	-0.0031340	0.0002498	618.6204	-12.5483373	0.0000000	5
SHAPEIT	SUPER	AMR - EUR	0	0.0005288	0.0002214	618.6204	2.3888142	0.1196902	5
SHAPEIT	SUPER	AMR - SAS	0	-0.0023104	0.0002369	618.6204	-9.7528012	0.0000000	5
SHAPEIT	SUPER	EAS - EUR	0	0.0036627	0.0002615	618.6204	14.0048548	0.0000000	5
SHAPEIT	SUPER	EAS - SAS	0	0.0008235	0.0002748	618.6204	2.9966330	0.0236668	5
SHAPEIT	SUPER	EUR - SAS	0	-0.0028392	0.0002493	618.6204	-11.3891895	0.0000000	5
Beagle	SUPER	AFR - AMR	0	-0.0010278	0.0001689	619.7714	-6.0861081	0.0000000	6
Beagle	SUPER	AFR - EAS	0	-0.0036264	0.0002094	619.7714	-17.3206822	0.0000000	6
Beagle	SUPER	AFR - EUR	0	-0.0006144	0.0001824	619.7714	-3.3679924	0.0071679	6
Beagle	SUPER	AFR - SAS	0	-0.0029280	0.0001972	619.7714	-14.8459920	0.0000000	6
Beagle	SUPER	AMR - EAS	0	-0.0025985	0.0002219	619.7714	-11.7108756	0.0000000	6
Beagle	SUPER	AMR - EUR	0	0.0004135	0.0001967	619.7714	2.1023116	0.2203142	6
Beagle	SUPER	AMR - SAS	0	-0.0019002	0.0002105	619.7714	-9.0281098	0.0000000	6
Beagle	SUPER	EAS - EUR	0	0.0030120	0.0002324	619.7714	12.9626300	0.0000000	6
Beagle	SUPER	EAS - SAS	0	0.0006983	0.0002442	619.7714	2.8602610	0.0353300	6
Beagle	SUPER	EUR - SAS	0	-0.0023136	0.0002215	619.7714	-10.4461174	0.0000000	6
Eagle	SUPER	AFR - AMR	0	-0.0014525	0.0001689	619.7714	-8.6006535	0.0000000	6
Eagle	SUPER	AFR - EAS	0	-0.0042507	0.0002094	619.7714	-20.3026035	0.0000000	6
Eagle	SUPER	AFR - EUR	0	-0.0010349	0.0001824	619.7714	-5.6728974	0.0000002	6
Eagle	SUPER	AFR - SAS	0	-0.0032724	0.0001972	619.7714	-16.5921877	0.0000000	6
Eagle	SUPER	AMR - EAS	0	-0.0027982	0.0002219	619.7714	-12.6106311	0.0000000	6
Eagle	SUPER	AMR - EUR	0	0.0004177	0.0001967	619.7714	2.1236894	0.2112593	6
Eagle	SUPER	AMR - SAS	0	-0.0018199	0.0002105	619.7714	-8.6467229	0.0000000	6
Eagle	SUPER	EAS - EUR	0	0.0032158	0.0002324	619.7714	13.8399410	0.0000000	6
Eagle	SUPER	EAS - SAS	0	0.0009783	0.0002442	619.7714	4.0067414	0.0006578	6
Eagle	SUPER	EUR - SAS	0	-0.0022376	0.0002215	619.7714	-10.1026708	0.0000000	6
SHAPEIT	SUPER	AFR - AMR	0	-0.0011273	0.0001689	619.7714	-6.6748165	0.0000000	6
SHAPEIT	SUPER	AFR - EAS	0	-0.0037636	0.0002094	619.7714	-17.9762149	0.0000000	6
SHAPEIT	SUPER	AFR - EUR	0	-0.0005196	0.0001824	619.7714	-2.8482309	0.0365645	6
SHAPEIT	SUPER	AFR - SAS	0	-0.0031023	0.0001972	619.7714	-15.7294721	0.0000000	6
SHAPEIT	SUPER	AMR - EAS	0	-0.0026363	0.0002219	619.7714	-11.8813333	0.0000000	6
SHAPEIT	SUPER	AMR - EUR	0	0.0006077	0.0001967	619.7714	3.0899647	0.0177762	6
SHAPEIT	SUPER	AMR - SAS	0	-0.0019750	0.0002105	619.7714	-9.3836041	0.0000000	6
SHAPEIT	SUPER	EAS - EUR	0	0.0032440	0.0002324	619.7714	13.9613549	0.0000000	6
SHAPEIT	SUPER	EAS - SAS	0	0.0006613	0.0002442	619.7714	2.7087206	0.0538020	6
SHAPEIT	SUPER	EUR - SAS	0	-0.0025827	0.0002215	619.7714	-11.6609377	0.0000000	6
Beagle	SUPER	AFR - AMR	0	-0.0011244	0.0001844	622.9174	-6.0965236	0.0000000	7
Beagle	SUPER	AFR - EAS	0	-0.0042376	0.0002286	622.9174	-18.5336840	0.0000000	7
Beagle	SUPER	AFR - EUR	0	-0.0006582	0.0001992	622.9174	-3.3037046	0.0089057	7
Beagle	SUPER	AFR - SAS	0	-0.0032267	0.0002154	622.9174	-14.9807430	0.0000000	7
Beagle	SUPER	AMR - EAS	0	-0.0031132	0.0002423	622.9174	-12.8474905	0.0000000	7
Beagle	SUPER	AMR - EUR	0	0.0004663	0.0002148	622.9174	2.1708866	0.1921619	7
Beagle	SUPER	AMR - SAS	0	-0.0021022	0.0002299	622.9174	-9.1460225	0.0000000	7
Beagle	SUPER	EAS - EUR	0	0.0035795	0.0002538	622.9174	14.1060761	0.0000000	7
Beagle	SUPER	EAS - SAS	0	0.0010110	0.0002666	622.9174	3.7915799	0.0015384	7
Beagle	SUPER	EUR - SAS	0	-0.0025685	0.0002419	622.9174	-10.6190609	0.0000000	7
Eagle	SUPER	AFR - AMR	0	-0.0014571	0.0001844	622.9174	-7.9002640	0.0000000	7
Eagle	SUPER	AFR - EAS	0	-0.0047337	0.0002286	622.9174	-20.7034351	0.0000000	7
Eagle	SUPER	AFR - EUR	0	-0.0011198	0.0001992	622.9174	-5.6209473	0.0000003	7
Eagle	SUPER	AFR - SAS	0	-0.0035554	0.0002154	622.9174	-16.5069426	0.0000000	7
Eagle	SUPER	AMR - EAS	0	-0.0032766	0.0002423	622.9174	-13.5219213	0.0000000	7
Eagle	SUPER	AMR - EUR	0	0.0003373	0.0002148	622.9174	1.5704299	0.5170067	7
Eagle	SUPER	AMR - SAS	0	-0.0020983	0.0002299	622.9174	-9.1288384	0.0000000	7
Eagle	SUPER	EAS - EUR	0	0.0036139	0.0002538	622.9174	14.2418953	0.0000000	7
Eagle	SUPER	EAS - SAS	0	0.0011784	0.0002666	622.9174	4.4193220	0.0001137	7
Eagle	SUPER	EUR - SAS	0	-0.0024356	0.0002419	622.9174	-10.0695494	0.0000000	7
SHAPEIT	SUPER	AFR - AMR	0	-0.0011969	0.0001844	622.9174	-6.4894864	0.0000000	7
SHAPEIT	SUPER	AFR - EAS	0	-0.0043577	0.0002286	622.9174	-19.0587872	0.0000000	7
SHAPEIT	SUPER	AFR - EUR	0	-0.0005605	0.0001992	622.9174	-2.8134642	0.0403378	7
SHAPEIT	SUPER	AFR - SAS	0	-0.0034356	0.0002154	622.9174	-15.9507131	0.0000000	7
SHAPEIT	SUPER	AMR - EAS	0	-0.0031608	0.0002423	622.9174	-13.0438658	0.0000000	7
SHAPEIT	SUPER	AMR - EUR	0	0.0006364	0.0002148	622.9174	2.9630642	0.0261650	7
SHAPEIT	SUPER	AMR - SAS	0	-0.0022387	0.0002299	622.9174	-9.7396305	0.0000000	7
SHAPEIT	SUPER	EAS - EUR	0	0.0037972	0.0002538	622.9174	14.9641009	0.0000000	7
SHAPEIT	SUPER	EAS - SAS	0	0.0009221	0.0002666	622.9174	3.4583276	0.0052416	7
SHAPEIT	SUPER	EUR - SAS	0	-0.0028751	0.0002419	622.9174	-11.8865845	0.0000000	7
Beagle	SUPER	AFR - AMR	0	-0.0014515	0.0001926	630.1012	-7.5359547	0.0000000	8
Beagle	SUPER	AFR - EAS	0	-0.0046079	0.0002388	630.1012	-19.2983258	0.0000000	8
Beagle	SUPER	AFR - EUR	0	-0.0009419	0.0002080	630.1012	-4.5272532	0.0000699	8
Beagle	SUPER	AFR - SAS	0	-0.0033096	0.0002249	630.1012	-14.7139826	0.0000000	8
Beagle	SUPER	AMR - EAS	0	-0.0031564	0.0002531	630.1012	-12.4733969	0.0000000	8
Beagle	SUPER	AMR - EUR	0	0.0005096	0.0002243	630.1012	2.2720546	0.1553620	8
Beagle	SUPER	AMR - SAS	0	-0.0018581	0.0002400	630.1012	-7.7410453	0.0000000	8
Beagle	SUPER	EAS - EUR	0	0.0036660	0.0002650	630.1012	13.8344658	0.0000000	8
Beagle	SUPER	EAS - SAS	0	0.0012983	0.0002784	630.1012	4.6627614	0.0000374	8
Beagle	SUPER	EUR - SAS	0	-0.0023677	0.0002526	630.1012	-9.3737543	0.0000000	8
Eagle	SUPER	AFR - AMR	0	-0.0020009	0.0001926	630.1012	-10.3885469	0.0000000	8
Eagle	SUPER	AFR - EAS	0	-0.0052729	0.0002388	630.1012	-22.0836020	0.0000000	8
Eagle	SUPER	AFR - EUR	0	-0.0015167	0.0002080	630.1012	-7.2904244	0.0000000	8
Eagle	SUPER	AFR - SAS	0	-0.0037314	0.0002249	630.1012	-16.5895812	0.0000000	8
Eagle	SUPER	AMR - EAS	0	-0.0032721	0.0002531	630.1012	-12.9303112	0.0000000	8
Eagle	SUPER	AMR - EUR	0	0.0004842	0.0002243	630.1012	2.1586537	0.1969751	8
Eagle	SUPER	AMR - SAS	0	-0.0017306	0.0002400	630.1012	-7.2096669	0.0000000	8
Eagle	SUPER	EAS - EUR	0	0.0037562	0.0002650	630.1012	14.1748115	0.0000000	8
Eagle	SUPER	EAS - SAS	0	0.0015415	0.0002784	630.1012	5.5360841	0.0000005	8
Eagle	SUPER	EUR - SAS	0	-0.0022147	0.0002526	630.1012	-8.7680936	0.0000000	8
SHAPEIT	SUPER	AFR - AMR	0	-0.0016379	0.0001926	630.1012	-8.5037740	0.0000000	8
SHAPEIT	SUPER	AFR - EAS	0	-0.0046015	0.0002388	630.1012	-19.2714578	0.0000000	8
SHAPEIT	SUPER	AFR - EUR	0	-0.0008229	0.0002080	630.1012	-3.9554378	0.0008075	8
SHAPEIT	SUPER	AFR - SAS	0	-0.0034985	0.0002249	630.1012	-15.5540680	0.0000000	8
SHAPEIT	SUPER	AMR - EAS	0	-0.0029636	0.0002531	630.1012	-11.7114181	0.0000000	8
SHAPEIT	SUPER	AMR - EUR	0	0.0008150	0.0002243	630.1012	3.6335453	0.0027878	8
SHAPEIT	SUPER	AMR - SAS	0	-0.0018607	0.0002400	630.1012	-7.7516758	0.0000000	8
SHAPEIT	SUPER	EAS - EUR	0	0.0037786	0.0002650	630.1012	14.2591805	0.0000000	8
SHAPEIT	SUPER	EAS - SAS	0	0.0011029	0.0002784	630.1012	3.9611044	0.0007894	8
SHAPEIT	SUPER	EUR - SAS	0	-0.0026756	0.0002526	630.1012	-10.5928058	0.0000000	8
Beagle	SUPER	AFR - AMR	0	-0.0009670	0.0002020	622.7189	-4.7865984	0.0000209	9
Beagle	SUPER	AFR - EAS	0	-0.0046635	0.0002504	622.7189	-18.6211034	0.0000000	9
Beagle	SUPER	AFR - EUR	0	-0.0009076	0.0002182	622.7189	-4.1592306	0.0003503	9
Beagle	SUPER	AFR - SAS	0	-0.0034326	0.0002359	622.7189	-14.5497417	0.0000000	9
Beagle	SUPER	AMR - EAS	0	-0.0036965	0.0002654	622.7189	-13.9269870	0.0000000	9
Beagle	SUPER	AMR - EUR	0	0.0000594	0.0002353	622.7189	0.2524599	0.9991039	9
Beagle	SUPER	AMR - SAS	0	-0.0024656	0.0002518	622.7189	-9.7932369	0.0000000	9
Beagle	SUPER	EAS - EUR	0	0.0037559	0.0002779	622.7189	13.5131842	0.0000000	9
Beagle	SUPER	EAS - SAS	0	0.0012309	0.0002921	622.7189	4.2147044	0.0002770	9
Beagle	SUPER	EUR - SAS	0	-0.0025250	0.0002649	622.7189	-9.5306177	0.0000000	9
Eagle	SUPER	AFR - AMR	0	-0.0014238	0.0002020	622.7189	-7.0478436	0.0000000	9
Eagle	SUPER	AFR - EAS	0	-0.0054288	0.0002504	622.7189	-21.6771002	0.0000000	9
Eagle	SUPER	AFR - EUR	0	-0.0014196	0.0002182	622.7189	-6.5055944	0.0000000	9
Eagle	SUPER	AFR - SAS	0	-0.0037863	0.0002359	622.7189	-16.0492072	0.0000000	9
Eagle	SUPER	AMR - EAS	0	-0.0040050	0.0002654	622.7189	-15.0894294	0.0000000	9
Eagle	SUPER	AMR - EUR	0	0.0000042	0.0002353	622.7189	0.0178652	1.0000000	9
Eagle	SUPER	AMR - SAS	0	-0.0023625	0.0002518	622.7189	-9.3838974	0.0000000	9
Eagle	SUPER	EAS - EUR	0	0.0040092	0.0002779	622.7189	14.4246920	0.0000000	9
Eagle	SUPER	EAS - SAS	0	0.0016425	0.0002921	622.7189	5.6240134	0.0000003	9
Eagle	SUPER	EUR - SAS	0	-0.0023667	0.0002649	622.7189	-8.9333145	0.0000000	9
SHAPEIT	SUPER	AFR - AMR	0	-0.0011353	0.0002020	622.7189	-5.6198815	0.0000003	9
SHAPEIT	SUPER	AFR - EAS	0	-0.0048050	0.0002504	622.7189	-19.1862858	0.0000000	9
SHAPEIT	SUPER	AFR - EUR	0	-0.0007718	0.0002182	622.7189	-3.5367896	0.0039676	9
SHAPEIT	SUPER	AFR - SAS	0	-0.0036449	0.0002359	622.7189	-15.4496997	0.0000000	9
SHAPEIT	SUPER	AMR - EAS	0	-0.0036697	0.0002654	622.7189	-13.8260429	0.0000000	9
SHAPEIT	SUPER	AMR - EUR	0	0.0003636	0.0002353	622.7189	1.5453785	0.5332710	9
SHAPEIT	SUPER	AMR - SAS	0	-0.0025096	0.0002518	622.7189	-9.9679242	0.0000000	9
SHAPEIT	SUPER	EAS - EUR	0	0.0040333	0.0002779	622.7189	14.5111111	0.0000000	9
SHAPEIT	SUPER	EAS - SAS	0	0.0011601	0.0002921	622.7189	3.9723762	0.0007553	9
SHAPEIT	SUPER	EUR - SAS	0	-0.0028731	0.0002649	622.7189	-10.8446819	0.0000000	9
Beagle	SUPER	AFR - AMR	0	-0.0010874	0.0001749	626.1417	-6.2164281	0.0000000	10
Beagle	SUPER	AFR - EAS	0	-0.0039478	0.0002168	626.1417	-18.2054827	0.0000000	10
Beagle	SUPER	AFR - EUR	0	-0.0006912	0.0001889	626.1417	-3.6581915	0.0025459	10
Beagle	SUPER	AFR - SAS	0	-0.0031931	0.0002043	626.1417	-15.6313950	0.0000000	10
Beagle	SUPER	AMR - EAS	0	-0.0028604	0.0002298	626.1417	-12.4465504	0.0000000	10
Beagle	SUPER	AMR - EUR	0	0.0003962	0.0002037	626.1417	1.9450439	0.2946378	10
Beagle	SUPER	AMR - SAS	0	-0.0021057	0.0002180	626.1417	-9.6595124	0.0000000	10
Beagle	SUPER	EAS - EUR	0	0.0032566	0.0002407	626.1417	13.5320479	0.0000000	10
Beagle	SUPER	EAS - SAS	0	0.0007547	0.0002529	626.1417	2.9845479	0.0245333	10
Beagle	SUPER	EUR - SAS	0	-0.0025019	0.0002294	626.1417	-10.9064875	0.0000000	10
Eagle	SUPER	AFR - AMR	0	-0.0015247	0.0001749	626.1417	-8.7164454	0.0000000	10
Eagle	SUPER	AFR - EAS	0	-0.0046306	0.0002168	626.1417	-21.3542536	0.0000000	10
Eagle	SUPER	AFR - EUR	0	-0.0011621	0.0001889	626.1417	-6.1505598	0.0000000	10
Eagle	SUPER	AFR - SAS	0	-0.0036710	0.0002043	626.1417	-17.9710118	0.0000000	10
Eagle	SUPER	AMR - EAS	0	-0.0031059	0.0002298	626.1417	-13.5147965	0.0000000	10
Eagle	SUPER	AMR - EUR	0	0.0003626	0.0002037	626.1417	1.7800623	0.3861436	10
Eagle	SUPER	AMR - SAS	0	-0.0021463	0.0002180	626.1417	-9.8458560	0.0000000	10
Eagle	SUPER	EAS - EUR	0	0.0034685	0.0002407	626.1417	14.4125238	0.0000000	10
Eagle	SUPER	EAS - SAS	0	0.0009596	0.0002529	626.1417	3.7947418	0.0015191	10
Eagle	SUPER	EUR - SAS	0	-0.0025089	0.0002294	626.1417	-10.9370712	0.0000000	10
SHAPEIT	SUPER	AFR - AMR	0	-0.0012013	0.0001749	626.1417	-6.8678015	0.0000000	10
SHAPEIT	SUPER	AFR - EAS	0	-0.0041689	0.0002168	626.1417	-19.2250673	0.0000000	10
SHAPEIT	SUPER	AFR - EUR	0	-0.0005814	0.0001889	626.1417	-3.0773001	0.0184835	10
SHAPEIT	SUPER	AFR - SAS	0	-0.0034282	0.0002043	626.1417	-16.7823108	0.0000000	10
SHAPEIT	SUPER	AMR - EAS	0	-0.0029676	0.0002298	626.1417	-12.9128181	0.0000000	10
SHAPEIT	SUPER	AMR - EUR	0	0.0006199	0.0002037	626.1417	3.0432112	0.0205333	10
SHAPEIT	SUPER	AMR - SAS	0	-0.0022269	0.0002180	626.1417	-10.2153282	0.0000000	10
SHAPEIT	SUPER	EAS - EUR	0	0.0035875	0.0002407	626.1417	14.9067938	0.0000000	10
SHAPEIT	SUPER	EAS - SAS	0	0.0007407	0.0002529	626.1417	2.9291549	0.0289217	10
SHAPEIT	SUPER	EUR - SAS	0	-0.0028467	0.0002294	626.1417	-12.4098040	0.0000000	10
Beagle	SUPER	AFR - AMR	0	-0.0014214	0.0001955	623.5183	-7.2691170	0.0000000	11
Beagle	SUPER	AFR - EAS	0	-0.0043086	0.0002424	623.5183	-17.7742435	0.0000000	11
Beagle	SUPER	AFR - EUR	0	-0.0008648	0.0002112	623.5183	-4.0946807	0.0004584	11
Beagle	SUPER	AFR - SAS	0	-0.0036206	0.0002284	623.5183	-15.8554625	0.0000000	11
Beagle	SUPER	AMR - EAS	0	-0.0028872	0.0002569	623.5183	-11.2384264	0.0000000	11
Beagle	SUPER	AMR - EUR	0	0.0005565	0.0002277	623.5183	2.4441503	0.1051370	11
Beagle	SUPER	AMR - SAS	0	-0.0021992	0.0002437	623.5183	-9.0247957	0.0000000	11
Beagle	SUPER	EAS - EUR	0	0.0034438	0.0002690	623.5183	12.8007987	0.0000000	11
Beagle	SUPER	EAS - SAS	0	0.0006880	0.0002827	623.5183	2.4337520	0.1077584	11
Beagle	SUPER	EUR - SAS	0	-0.0027558	0.0002564	623.5183	-10.7465072	0.0000000	11
Eagle	SUPER	AFR - AMR	0	-0.0018680	0.0001955	623.5183	-9.5529109	0.0000000	11
Eagle	SUPER	AFR - EAS	0	-0.0049399	0.0002424	623.5183	-20.3782727	0.0000000	11
Eagle	SUPER	AFR - EUR	0	-0.0014279	0.0002112	623.5183	-6.7606011	0.0000000	11
Eagle	SUPER	AFR - SAS	0	-0.0040539	0.0002284	623.5183	-17.7526824	0.0000000	11
Eagle	SUPER	AMR - EAS	0	-0.0030719	0.0002569	623.5183	-11.9572470	0.0000000	11
Eagle	SUPER	AMR - EUR	0	0.0004400	0.0002277	623.5183	1.9325106	0.3011351	11
Eagle	SUPER	AMR - SAS	0	-0.0021859	0.0002437	623.5183	-8.9700839	0.0000000	11
Eagle	SUPER	EAS - EUR	0	0.0035119	0.0002690	623.5183	13.0541821	0.0000000	11
Eagle	SUPER	EAS - SAS	0	0.0008860	0.0002827	623.5183	3.1341868	0.0154671	11
Eagle	SUPER	EUR - SAS	0	-0.0026260	0.0002564	623.5183	-10.2401994	0.0000000	11
SHAPEIT	SUPER	AFR - AMR	0	-0.0015101	0.0001955	623.5183	-7.7227364	0.0000000	11
SHAPEIT	SUPER	AFR - EAS	0	-0.0044835	0.0002424	623.5183	-18.4954733	0.0000000	11
SHAPEIT	SUPER	AFR - EUR	0	-0.0007548	0.0002112	623.5183	-3.5735260	0.0034748	11
SHAPEIT	SUPER	AFR - SAS	0	-0.0037782	0.0002284	623.5183	-16.5455945	0.0000000	11
SHAPEIT	SUPER	AMR - EAS	0	-0.0029734	0.0002569	623.5183	-11.5736924	0.0000000	11
SHAPEIT	SUPER	AMR - EUR	0	0.0007553	0.0002277	623.5183	3.3170905	0.0085143	11
SHAPEIT	SUPER	AMR - SAS	0	-0.0022681	0.0002437	623.5183	-9.3075066	0.0000000	11
SHAPEIT	SUPER	EAS - EUR	0	0.0037287	0.0002690	623.5183	13.8598135	0.0000000	11
SHAPEIT	SUPER	EAS - SAS	0	0.0007052	0.0002827	623.5183	2.4947337	0.0930927	11
SHAPEIT	SUPER	EUR - SAS	0	-0.0030235	0.0002564	623.5183	-11.7903015	0.0000000	11
Beagle	SUPER	AFR - AMR	0	-0.0012389	0.0002167	630.4754	-5.7179370	0.0000002	12
Beagle	SUPER	AFR - EAS	0	-0.0043150	0.0002686	630.4754	-16.0637948	0.0000000	12
Beagle	SUPER	AFR - EUR	0	-0.0008773	0.0002340	630.4754	-3.7484051	0.0018128	12
Beagle	SUPER	AFR - SAS	0	-0.0037226	0.0002530	630.4754	-14.7116726	0.0000000	12
Beagle	SUPER	AMR - EAS	0	-0.0030760	0.0002847	630.4754	-10.8051470	0.0000000	12
Beagle	SUPER	AMR - EUR	0	0.0003617	0.0002523	630.4754	1.4332954	0.6063265	12
Beagle	SUPER	AMR - SAS	0	-0.0024837	0.0002700	630.4754	-9.1976661	0.0000000	12
Beagle	SUPER	EAS - EUR	0	0.0034377	0.0002981	630.4754	11.5314557	0.0000000	12
Beagle	SUPER	EAS - SAS	0	0.0005923	0.0003132	630.4754	1.8909609	0.3232130	12
Beagle	SUPER	EUR - SAS	0	-0.0028453	0.0002842	630.4754	-10.0131858	0.0000000	12
Eagle	SUPER	AFR - AMR	0	-0.0017589	0.0002167	630.4754	-8.1177207	0.0000000	12
Eagle	SUPER	AFR - EAS	0	-0.0050468	0.0002686	630.4754	-18.7882745	0.0000000	12
Eagle	SUPER	AFR - EUR	0	-0.0014243	0.0002340	630.4754	-6.0857113	0.0000000	12
Eagle	SUPER	AFR - SAS	0	-0.0039907	0.0002530	630.4754	-15.7709406	0.0000000	12
Eagle	SUPER	AMR - EAS	0	-0.0032879	0.0002847	630.4754	-11.5493379	0.0000000	12
Eagle	SUPER	AMR - EUR	0	0.0003346	0.0002523	630.4754	1.3260696	0.6750394	12
Eagle	SUPER	AMR - SAS	0	-0.0022318	0.0002700	630.4754	-8.2646700	0.0000000	12
Eagle	SUPER	EAS - EUR	0	0.0036225	0.0002981	630.4754	12.1513612	0.0000000	12
Eagle	SUPER	EAS - SAS	0	0.0010561	0.0003132	630.4754	3.3715777	0.0070742	12
Eagle	SUPER	EUR - SAS	0	-0.0025664	0.0002842	630.4754	-9.0313541	0.0000000	12
SHAPEIT	SUPER	AFR - AMR	0	-0.0014038	0.0002167	630.4754	-6.4789055	0.0000000	12
SHAPEIT	SUPER	AFR - EAS	0	-0.0045536	0.0002686	630.4754	-16.9521030	0.0000000	12
SHAPEIT	SUPER	AFR - EUR	0	-0.0008387	0.0002340	630.4754	-3.5832924	0.0033511	12
SHAPEIT	SUPER	AFR - SAS	0	-0.0040962	0.0002530	630.4754	-16.1878915	0.0000000	12
SHAPEIT	SUPER	AMR - EAS	0	-0.0031498	0.0002847	630.4754	-11.0641321	0.0000000	12
SHAPEIT	SUPER	AMR - EUR	0	0.0005652	0.0002523	630.4754	2.2399150	0.1664425	12
SHAPEIT	SUPER	AMR - SAS	0	-0.0026924	0.0002700	630.4754	-9.9703718	0.0000000	12
SHAPEIT	SUPER	EAS - EUR	0	0.0037149	0.0002981	630.4754	12.4614929	0.0000000	12
SHAPEIT	SUPER	EAS - SAS	0	0.0004574	0.0003132	630.4754	1.4602176	0.5888040	12
SHAPEIT	SUPER	EUR - SAS	0	-0.0032575	0.0002842	630.4754	-11.4637287	0.0000000	12
Beagle	SUPER	AFR - AMR	0	-0.0010116	0.0001894	639.1797	-5.3420672	0.0000013	13
Beagle	SUPER	AFR - EAS	0	-0.0041622	0.0002348	639.1797	-17.7301525	0.0000000	13
Beagle	SUPER	AFR - EUR	0	-0.0008443	0.0002045	639.1797	-4.1278110	0.0003983	13
Beagle	SUPER	AFR - SAS	0	-0.0031188	0.0002211	639.1797	-14.1030464	0.0000000	13
Beagle	SUPER	AMR - EAS	0	-0.0031506	0.0002488	639.1797	-12.6635410	0.0000000	13
Beagle	SUPER	AMR - EUR	0	0.0001673	0.0002205	639.1797	0.7586019	0.9422196	13
Beagle	SUPER	AMR - SAS	0	-0.0021072	0.0002360	639.1797	-8.9289446	0.0000000	13
Beagle	SUPER	EAS - EUR	0	0.0033179	0.0002605	639.1797	12.7350603	0.0000000	13
Beagle	SUPER	EAS - SAS	0	0.0010434	0.0002738	639.1797	3.8115371	0.0014213	13
Beagle	SUPER	EUR - SAS	0	-0.0022745	0.0002483	639.1797	-9.1587208	0.0000000	13
Eagle	SUPER	AFR - AMR	0	-0.0014869	0.0001894	639.1797	-7.8521398	0.0000000	13
Eagle	SUPER	AFR - EAS	0	-0.0049285	0.0002348	639.1797	-20.9943993	0.0000000	13
Eagle	SUPER	AFR - EUR	0	-0.0013932	0.0002045	639.1797	-6.8115103	0.0000000	13
Eagle	SUPER	AFR - SAS	0	-0.0038451	0.0002211	639.1797	-17.3873847	0.0000000	13
Eagle	SUPER	AMR - EAS	0	-0.0034416	0.0002488	639.1797	-13.8330924	0.0000000	13
Eagle	SUPER	AMR - EUR	0	0.0000937	0.0002205	639.1797	0.4247838	0.9931976	13
Eagle	SUPER	AMR - SAS	0	-0.0023582	0.0002360	639.1797	-9.9924832	0.0000000	13
Eagle	SUPER	EAS - EUR	0	0.0035353	0.0002605	639.1797	13.5693745	0.0000000	13
Eagle	SUPER	EAS - SAS	0	0.0010834	0.0002738	639.1797	3.9576118	0.0007994	13
Eagle	SUPER	EUR - SAS	0	-0.0024518	0.0002483	639.1797	-9.8729767	0.0000000	13
SHAPEIT	SUPER	AFR - AMR	0	-0.0011737	0.0001894	639.1797	-6.1981607	0.0000000	13
SHAPEIT	SUPER	AFR - EAS	0	-0.0042709	0.0002348	639.1797	-18.1933113	0.0000000	13
SHAPEIT	SUPER	AFR - EUR	0	-0.0007486	0.0002045	639.1797	-3.6598952	0.0025260	13
SHAPEIT	SUPER	AFR - SAS	0	-0.0034515	0.0002211	639.1797	-15.6076484	0.0000000	13
SHAPEIT	SUPER	AMR - EAS	0	-0.0030972	0.0002488	639.1797	-12.4489696	0.0000000	13
SHAPEIT	SUPER	AMR - EUR	0	0.0004251	0.0002205	639.1797	1.9277768	0.3035797	13
SHAPEIT	SUPER	AMR - SAS	0	-0.0022778	0.0002360	639.1797	-9.6519183	0.0000000	13
SHAPEIT	SUPER	EAS - EUR	0	0.0035223	0.0002605	639.1797	13.5197433	0.0000000	13
SHAPEIT	SUPER	EAS - SAS	0	0.0008194	0.0002738	639.1797	2.9932930	0.0238810	13
SHAPEIT	SUPER	EUR - SAS	0	-0.0027029	0.0002483	639.1797	-10.8839383	0.0000000	13
Beagle	SUPER	AFR - AMR	0	-0.0014573	0.0002031	629.1835	-7.1750953	0.0000000	14
Beagle	SUPER	AFR - EAS	0	-0.0041591	0.0002518	629.1835	-16.5181164	0.0000000	14
Beagle	SUPER	AFR - EUR	0	-0.0007848	0.0002194	629.1835	-3.5770367	0.0034287	14
Beagle	SUPER	AFR - SAS	0	-0.0034408	0.0002372	629.1835	-14.5066154	0.0000000	14
Beagle	SUPER	AMR - EAS	0	-0.0027018	0.0002669	629.1835	-10.1247544	0.0000000	14
Beagle	SUPER	AMR - EUR	0	0.0006726	0.0002365	629.1835	2.8435576	0.0370395	14
Beagle	SUPER	AMR - SAS	0	-0.0019835	0.0002531	629.1835	-7.8362844	0.0000000	14
Beagle	SUPER	EAS - EUR	0	0.0033744	0.0002794	629.1835	12.0753608	0.0000000	14
Beagle	SUPER	EAS - SAS	0	0.0007183	0.0002936	629.1835	2.4461938	0.1046155	14
Beagle	SUPER	EUR - SAS	0	-0.0026561	0.0002664	629.1835	-9.9717311	0.0000000	14
Eagle	SUPER	AFR - AMR	0	-0.0019261	0.0002031	629.1835	-9.4832583	0.0000000	14
Eagle	SUPER	AFR - EAS	0	-0.0050255	0.0002518	629.1835	-19.9590968	0.0000000	14
Eagle	SUPER	AFR - EUR	0	-0.0013647	0.0002194	629.1835	-6.2207193	0.0000000	14
Eagle	SUPER	AFR - SAS	0	-0.0038465	0.0002372	629.1835	-16.2166672	0.0000000	14
Eagle	SUPER	AMR - EAS	0	-0.0030994	0.0002669	629.1835	-11.6147426	0.0000000	14
Eagle	SUPER	AMR - EUR	0	0.0005614	0.0002365	629.1835	2.3734712	0.1239617	14
Eagle	SUPER	AMR - SAS	0	-0.0019203	0.0002531	629.1835	-7.5866305	0.0000000	14
Eagle	SUPER	EAS - EUR	0	0.0036608	0.0002794	629.1835	13.1003372	0.0000000	14
Eagle	SUPER	EAS - SAS	0	0.0011791	0.0002936	629.1835	4.0155222	0.0006337	14
Eagle	SUPER	EUR - SAS	0	-0.0024817	0.0002664	629.1835	-9.3170689	0.0000000	14
SHAPEIT	SUPER	AFR - AMR	0	-0.0016062	0.0002031	629.1835	-7.9083633	0.0000000	14
SHAPEIT	SUPER	AFR - EAS	0	-0.0044053	0.0002518	629.1835	-17.4959964	0.0000000	14
SHAPEIT	SUPER	AFR - EUR	0	-0.0007646	0.0002194	629.1835	-3.4850092	0.0047685	14
SHAPEIT	SUPER	AFR - SAS	0	-0.0036953	0.0002372	629.1835	-15.5792335	0.0000000	14
SHAPEIT	SUPER	AMR - EAS	0	-0.0027991	0.0002669	629.1835	-10.4893395	0.0000000	14
SHAPEIT	SUPER	AMR - EUR	0	0.0008417	0.0002365	629.1835	3.5585990	0.0036655	14
SHAPEIT	SUPER	AMR - SAS	0	-0.0020890	0.0002531	629.1835	-8.2530176	0.0000000	14
SHAPEIT	SUPER	EAS - EUR	0	0.0036408	0.0002794	629.1835	13.0287286	0.0000000	14
SHAPEIT	SUPER	EAS - SAS	0	0.0007101	0.0002936	629.1835	2.4182868	0.1117392	14
SHAPEIT	SUPER	EUR - SAS	0	-0.0029307	0.0002664	629.1835	-11.0026781	0.0000000	14
Beagle	SUPER	AFR - AMR	0	-0.0010614	0.0002245	625.9843	-4.7276363	0.0000276	15
Beagle	SUPER	AFR - EAS	0	-0.0047660	0.0002783	625.9843	-17.1244395	0.0000000	15
Beagle	SUPER	AFR - EUR	0	-0.0011094	0.0002425	625.9843	-4.5747598	0.0000563	15
Beagle	SUPER	AFR - SAS	0	-0.0036459	0.0002622	625.9843	-13.9065239	0.0000000	15
Beagle	SUPER	AMR - EAS	0	-0.0037046	0.0002950	625.9843	-12.5596691	0.0000000	15
Beagle	SUPER	AMR - EUR	0	-0.0000480	0.0002614	625.9843	-0.1836016	0.9997458	15
Beagle	SUPER	AMR - SAS	0	-0.0025846	0.0002798	625.9843	-9.2378127	0.0000000	15
Beagle	SUPER	EAS - EUR	0	0.0036566	0.0003089	625.9843	11.8383898	0.0000000	15
Beagle	SUPER	EAS - SAS	0	0.0011200	0.0003246	625.9843	3.4508776	0.0053787	15
Beagle	SUPER	EUR - SAS	0	-0.0025366	0.0002944	625.9843	-8.6155968	0.0000000	15
Eagle	SUPER	AFR - AMR	0	-0.0014429	0.0002245	625.9843	-6.4272183	0.0000000	15
Eagle	SUPER	AFR - EAS	0	-0.0053909	0.0002783	625.9843	-19.3698530	0.0000000	15
Eagle	SUPER	AFR - EUR	0	-0.0015275	0.0002425	625.9843	-6.2991073	0.0000000	15
Eagle	SUPER	AFR - SAS	0	-0.0041471	0.0002622	625.9843	-15.8180651	0.0000000	15
Eagle	SUPER	AMR - EAS	0	-0.0039480	0.0002950	625.9843	-13.3847692	0.0000000	15
Eagle	SUPER	AMR - EUR	0	-0.0000846	0.0002614	625.9843	-0.3235557	0.9976281	15
Eagle	SUPER	AMR - SAS	0	-0.0027042	0.0002798	625.9843	-9.6652951	0.0000000	15
Eagle	SUPER	EAS - EUR	0	0.0038634	0.0003089	625.9843	12.5078580	0.0000000	15
Eagle	SUPER	EAS - SAS	0	0.0012438	0.0003246	625.9843	3.8322244	0.0013141	15
Eagle	SUPER	EUR - SAS	0	-0.0026196	0.0002944	625.9843	-8.8975567	0.0000000	15
SHAPEIT	SUPER	AFR - AMR	0	-0.0012750	0.0002245	625.9843	-5.6793027	0.0000002	15
SHAPEIT	SUPER	AFR - EAS	0	-0.0050149	0.0002783	625.9843	-18.0189972	0.0000000	15
SHAPEIT	SUPER	AFR - EUR	0	-0.0010286	0.0002425	625.9843	-4.2419313	0.0002465	15
SHAPEIT	SUPER	AFR - SAS	0	-0.0040806	0.0002622	625.9843	-15.5645729	0.0000000	15
SHAPEIT	SUPER	AMR - EAS	0	-0.0037399	0.0002950	625.9843	-12.6794070	0.0000000	15
SHAPEIT	SUPER	AMR - EUR	0	0.0002464	0.0002614	625.9843	0.9423430	0.8802320	15
SHAPEIT	SUPER	AMR - SAS	0	-0.0028056	0.0002798	625.9843	-10.0278877	0.0000000	15
SHAPEIT	SUPER	EAS - EUR	0	0.0039863	0.0003089	625.9843	12.9057295	0.0000000	15
SHAPEIT	SUPER	EAS - SAS	0	0.0009343	0.0003246	625.9843	2.8786119	0.0335069	15
SHAPEIT	SUPER	EUR - SAS	0	-0.0030520	0.0002944	625.9843	-10.3661934	0.0000000	15
Beagle	SUPER	AFR - AMR	0	-0.0014752	0.0002468	635.1038	-5.9760746	0.0000000	16
Beagle	SUPER	AFR - EAS	0	-0.0052671	0.0003060	635.1038	-17.2117779	0.0000000	16
Beagle	SUPER	AFR - EUR	0	-0.0008846	0.0002666	635.1038	-3.3177969	0.0084863	16
Beagle	SUPER	AFR - SAS	0	-0.0040924	0.0002883	635.1038	-14.1961532	0.0000000	16
Beagle	SUPER	AMR - EAS	0	-0.0037919	0.0003243	635.1038	-11.6918664	0.0000000	16
Beagle	SUPER	AMR - EUR	0	0.0005905	0.0002875	635.1038	2.0543818	0.2415070	16
Beagle	SUPER	AMR - SAS	0	-0.0026172	0.0003076	635.1038	-8.5074612	0.0000000	16
Beagle	SUPER	EAS - EUR	0	0.0043825	0.0003396	635.1038	12.9039097	0.0000000	16
Beagle	SUPER	EAS - SAS	0	0.0011747	0.0003569	635.1038	3.2918106	0.0092581	16
Beagle	SUPER	EUR - SAS	0	-0.0032078	0.0003237	635.1038	-9.9087891	0.0000000	16
Eagle	SUPER	AFR - AMR	0	-0.0017876	0.0002468	635.1038	-7.2415754	0.0000000	16
Eagle	SUPER	AFR - EAS	0	-0.0058365	0.0003060	635.1038	-19.0723537	0.0000000	16
Eagle	SUPER	AFR - EUR	0	-0.0015439	0.0002666	635.1038	-5.7903934	0.0000001	16
Eagle	SUPER	AFR - SAS	0	-0.0040591	0.0002883	635.1038	-14.0806415	0.0000000	16
Eagle	SUPER	AMR - EAS	0	-0.0040489	0.0003243	635.1038	-12.4842363	0.0000000	16
Eagle	SUPER	AMR - EUR	0	0.0002437	0.0002875	635.1038	0.8476218	0.9155117	16
Eagle	SUPER	AMR - SAS	0	-0.0022715	0.0003076	635.1038	-7.3837761	0.0000000	16
Eagle	SUPER	EAS - EUR	0	0.0042926	0.0003396	635.1038	12.6391805	0.0000000	16
Eagle	SUPER	EAS - SAS	0	0.0017774	0.0003569	635.1038	4.9805965	0.0000081	16
Eagle	SUPER	EUR - SAS	0	-0.0025152	0.0003237	635.1038	-7.7694042	0.0000000	16
SHAPEIT	SUPER	AFR - AMR	0	-0.0017040	0.0002468	635.1038	-6.9028705	0.0000000	16
SHAPEIT	SUPER	AFR - EAS	0	-0.0054842	0.0003060	635.1038	-17.9211335	0.0000000	16
SHAPEIT	SUPER	AFR - EUR	0	-0.0010933	0.0002666	635.1038	-4.1003796	0.0004468	16
SHAPEIT	SUPER	AFR - SAS	0	-0.0042918	0.0002883	635.1038	-14.8879181	0.0000000	16
SHAPEIT	SUPER	AMR - EAS	0	-0.0037802	0.0003243	635.1038	-11.6557840	0.0000000	16
SHAPEIT	SUPER	AMR - EUR	0	0.0006107	0.0002875	635.1038	2.1243569	0.2109475	16
SHAPEIT	SUPER	AMR - SAS	0	-0.0025878	0.0003076	635.1038	-8.4120234	0.0000000	16
SHAPEIT	SUPER	EAS - EUR	0	0.0043909	0.0003396	635.1038	12.9286797	0.0000000	16
SHAPEIT	SUPER	EAS - SAS	0	0.0011924	0.0003569	635.1038	3.3412908	0.0078393	16
SHAPEIT	SUPER	EUR - SAS	0	-0.0031985	0.0003237	635.1038	-9.8802303	0.0000000	16
Beagle	SUPER	AFR - AMR	0	-0.0014479	0.0002472	628.8503	-5.8566941	0.0000001	17
Beagle	SUPER	AFR - EAS	0	-0.0056484	0.0003065	628.8503	-18.4294160	0.0000000	17
Beagle	SUPER	AFR - EUR	0	-0.0011418	0.0002670	628.8503	-4.2757689	0.0002130	17
Beagle	SUPER	AFR - SAS	0	-0.0041924	0.0002887	628.8503	-14.5208586	0.0000000	17
Beagle	SUPER	AMR - EAS	0	-0.0042004	0.0003248	628.8503	-12.9316463	0.0000000	17
Beagle	SUPER	AMR - EUR	0	0.0003061	0.0002879	628.8503	1.0632881	0.8252635	17
Beagle	SUPER	AMR - SAS	0	-0.0027445	0.0003081	628.8503	-8.9075221	0.0000000	17
Beagle	SUPER	EAS - EUR	0	0.0045066	0.0003401	628.8503	13.2489718	0.0000000	17
Beagle	SUPER	EAS - SAS	0	0.0014560	0.0003574	628.8503	4.0736608	0.0004995	17
Beagle	SUPER	EUR - SAS	0	-0.0030506	0.0003242	628.8503	-9.4089123	0.0000000	17
Eagle	SUPER	AFR - AMR	0	-0.0017465	0.0002472	628.8503	-7.0645036	0.0000000	17
Eagle	SUPER	AFR - EAS	0	-0.0061128	0.0003065	628.8503	-19.9446338	0.0000000	17
Eagle	SUPER	AFR - EUR	0	-0.0015395	0.0002670	628.8503	-5.7651733	0.0000001	17
Eagle	SUPER	AFR - SAS	0	-0.0045982	0.0002887	628.8503	-15.9262824	0.0000000	17
Eagle	SUPER	AMR - EAS	0	-0.0043662	0.0003248	628.8503	-13.4420597	0.0000000	17
Eagle	SUPER	AMR - EUR	0	0.0002070	0.0002879	628.8503	0.7189578	0.9521363	17
Eagle	SUPER	AMR - SAS	0	-0.0028516	0.0003081	628.8503	-9.2553411	0.0000000	17
Eagle	SUPER	EAS - EUR	0	0.0045732	0.0003401	628.8503	13.4449481	0.0000000	17
Eagle	SUPER	EAS - SAS	0	0.0015146	0.0003574	628.8503	4.2376915	0.0002508	17
Eagle	SUPER	EUR - SAS	0	-0.0030586	0.0003242	628.8503	-9.4336907	0.0000000	17
SHAPEIT	SUPER	AFR - AMR	0	-0.0014701	0.0002472	628.8503	-5.9463243	0.0000000	17
SHAPEIT	SUPER	AFR - EAS	0	-0.0056849	0.0003065	628.8503	-18.5484581	0.0000000	17
SHAPEIT	SUPER	AFR - EUR	0	-0.0009867	0.0002670	628.8503	-3.6947700	0.0022204	17
SHAPEIT	SUPER	AFR - SAS	0	-0.0043024	0.0002887	628.8503	-14.9019417	0.0000000	17
SHAPEIT	SUPER	AMR - EAS	0	-0.0042148	0.0003248	628.8503	-12.9757506	0.0000000	17
SHAPEIT	SUPER	AMR - EUR	0	0.0004834	0.0002879	628.8503	1.6791685	0.4476166	17
SHAPEIT	SUPER	AMR - SAS	0	-0.0028323	0.0003081	628.8503	-9.1927013	0.0000000	17
SHAPEIT	SUPER	EAS - EUR	0	0.0046982	0.0003401	628.8503	13.8123685	0.0000000	17
SHAPEIT	SUPER	EAS - SAS	0	0.0013824	0.0003574	628.8503	3.8679043	0.0011428	17
SHAPEIT	SUPER	EUR - SAS	0	-0.0033158	0.0003242	628.8503	-10.2267934	0.0000000	17
Beagle	SUPER	AFR - AMR	0	-0.0015084	0.0001993	629.0274	-7.5676517	0.0000000	18
Beagle	SUPER	AFR - EAS	0	-0.0047960	0.0002471	629.0274	-19.4097899	0.0000000	18
Beagle	SUPER	AFR - EUR	0	-0.0011030	0.0002153	629.0274	-5.1233338	0.0000040	18
Beagle	SUPER	AFR - SAS	0	-0.0036308	0.0002328	629.0274	-15.5986571	0.0000000	18
Beagle	SUPER	AMR - EAS	0	-0.0032877	0.0002619	629.0274	-12.5544450	0.0000000	18
Beagle	SUPER	AMR - EUR	0	0.0004053	0.0002321	629.0274	1.7463725	0.4062741	18
Beagle	SUPER	AMR - SAS	0	-0.0021225	0.0002484	629.0274	-8.5446072	0.0000000	18
Beagle	SUPER	EAS - EUR	0	0.0036930	0.0002742	629.0274	13.4669262	0.0000000	18
Beagle	SUPER	EAS - SAS	0	0.0011652	0.0002881	629.0274	4.0437078	0.0005649	18
Beagle	SUPER	EUR - SAS	0	-0.0025278	0.0002614	629.0274	-9.6705886	0.0000000	18
Eagle	SUPER	AFR - AMR	0	-0.0018831	0.0001993	629.0274	-9.4479626	0.0000000	18
Eagle	SUPER	AFR - EAS	0	-0.0054796	0.0002471	629.0274	-22.1761324	0.0000000	18
Eagle	SUPER	AFR - EUR	0	-0.0016680	0.0002153	629.0274	-7.7474975	0.0000000	18
Eagle	SUPER	AFR - SAS	0	-0.0039868	0.0002328	629.0274	-17.1281809	0.0000000	18
Eagle	SUPER	AMR - EAS	0	-0.0035964	0.0002619	629.0274	-13.7335174	0.0000000	18
Eagle	SUPER	AMR - EUR	0	0.0002152	0.0002321	629.0274	0.9269811	0.8864313	18
Eagle	SUPER	AMR - SAS	0	-0.0021037	0.0002484	629.0274	-8.4690977	0.0000000	18
Eagle	SUPER	EAS - EUR	0	0.0038116	0.0002742	629.0274	13.8993445	0.0000000	18
Eagle	SUPER	EAS - SAS	0	0.0014927	0.0002881	629.0274	5.1803522	0.0000030	18
Eagle	SUPER	EUR - SAS	0	-0.0023189	0.0002614	629.0274	-8.8712456	0.0000000	18
SHAPEIT	SUPER	AFR - AMR	0	-0.0016083	0.0001993	629.0274	-8.0689797	0.0000000	18
SHAPEIT	SUPER	AFR - EAS	0	-0.0048672	0.0002471	629.0274	-19.6978321	0.0000000	18
SHAPEIT	SUPER	AFR - EUR	0	-0.0009872	0.0002153	629.0274	-4.5852150	0.0000536	18
SHAPEIT	SUPER	AFR - SAS	0	-0.0037775	0.0002328	629.0274	-16.2286496	0.0000000	18
SHAPEIT	SUPER	AMR - EAS	0	-0.0032589	0.0002619	629.0274	-12.4446596	0.0000000	18
SHAPEIT	SUPER	AMR - EUR	0	0.0006211	0.0002321	629.0274	2.6760167	0.0586925	18
SHAPEIT	SUPER	AMR - SAS	0	-0.0021692	0.0002484	629.0274	-8.7326821	0.0000000	18
SHAPEIT	SUPER	EAS - EUR	0	0.0038800	0.0002742	629.0274	14.1489358	0.0000000	18
SHAPEIT	SUPER	EAS - SAS	0	0.0010897	0.0002881	629.0274	3.7818038	0.0015960	18
SHAPEIT	SUPER	EUR - SAS	0	-0.0027903	0.0002614	629.0274	-10.6748020	0.0000000	18
Beagle	SUPER	AFR - AMR	0	-0.0013213	0.0002242	634.4979	-5.8929134	0.0000001	19
Beagle	SUPER	AFR - EAS	0	-0.0050518	0.0002780	634.4979	-18.1740966	0.0000000	19
Beagle	SUPER	AFR - EUR	0	-0.0009680	0.0002422	634.4979	-3.9968421	0.0006830	19
Beagle	SUPER	AFR - SAS	0	-0.0035872	0.0002618	634.4979	-13.6997028	0.0000000	19
Beagle	SUPER	AMR - EAS	0	-0.0037304	0.0002946	634.4979	-12.6631694	0.0000000	19
Beagle	SUPER	AMR - EUR	0	0.0003533	0.0002611	634.4979	1.3531124	0.6579387	19
Beagle	SUPER	AMR - SAS	0	-0.0022659	0.0002794	634.4979	-8.1089849	0.0000000	19
Beagle	SUPER	EAS - EUR	0	0.0040838	0.0003085	634.4979	13.2378978	0.0000000	19
Beagle	SUPER	EAS - SAS	0	0.0014645	0.0003242	634.4979	4.5180460	0.0000728	19
Beagle	SUPER	EUR - SAS	0	-0.0026192	0.0002941	634.4979	-8.9074205	0.0000000	19
Eagle	SUPER	AFR - AMR	0	-0.0017241	0.0002242	634.4979	-7.6891767	0.0000000	19
Eagle	SUPER	AFR - EAS	0	-0.0055256	0.0002780	634.4979	-19.8788073	0.0000000	19
Eagle	SUPER	AFR - EUR	0	-0.0013803	0.0002422	634.4979	-5.6990356	0.0000002	19
Eagle	SUPER	AFR - SAS	0	-0.0038162	0.0002618	634.4979	-14.5740844	0.0000000	19
Eagle	SUPER	AMR - EAS	0	-0.0038015	0.0002946	634.4979	-12.9044968	0.0000000	19
Eagle	SUPER	AMR - EUR	0	0.0003438	0.0002611	634.4979	1.3167309	0.6808961	19
Eagle	SUPER	AMR - SAS	0	-0.0020921	0.0002794	634.4979	-7.4870059	0.0000000	19
Eagle	SUPER	EAS - EUR	0	0.0041453	0.0003085	634.4979	13.4375588	0.0000000	19
Eagle	SUPER	EAS - SAS	0	0.0017094	0.0003242	634.4979	5.2735435	0.0000018	19
Eagle	SUPER	EUR - SAS	0	-0.0024359	0.0002941	634.4979	-8.2840530	0.0000000	19
SHAPEIT	SUPER	AFR - AMR	0	-0.0014333	0.0002242	634.4979	-6.3923738	0.0000000	19
SHAPEIT	SUPER	AFR - EAS	0	-0.0052570	0.0002780	634.4979	-18.9124522	0.0000000	19
SHAPEIT	SUPER	AFR - EUR	0	-0.0009033	0.0002422	634.4979	-3.7298200	0.0019443	19
SHAPEIT	SUPER	AFR - SAS	0	-0.0038854	0.0002618	634.4979	-14.8386242	0.0000000	19
SHAPEIT	SUPER	AMR - EAS	0	-0.0038237	0.0002946	634.4979	-12.9797041	0.0000000	19
SHAPEIT	SUPER	AMR - EUR	0	0.0005300	0.0002611	634.4979	2.0296942	0.2529362	19
SHAPEIT	SUPER	AMR - SAS	0	-0.0024522	0.0002794	634.4979	-8.7754567	0.0000000	19
SHAPEIT	SUPER	EAS - EUR	0	0.0043537	0.0003085	634.4979	14.1128280	0.0000000	19
SHAPEIT	SUPER	EAS - SAS	0	0.0013715	0.0003242	634.4979	4.2311831	0.0002576	19
SHAPEIT	SUPER	EUR - SAS	0	-0.0029821	0.0002941	634.4979	-10.1415417	0.0000000	19
Beagle	SUPER	AFR - AMR	0	-0.0017747	0.0002477	624.9958	-7.1648970	0.0000000	20
Beagle	SUPER	AFR - EAS	0	-0.0057185	0.0003071	624.9958	-18.6226969	0.0000000	20
Beagle	SUPER	AFR - EUR	0	-0.0010484	0.0002676	624.9958	-3.9184499	0.0009367	20
Beagle	SUPER	AFR - SAS	0	-0.0040930	0.0002893	624.9958	-14.1496900	0.0000000	20
Beagle	SUPER	AMR - EAS	0	-0.0039438	0.0003254	624.9958	-12.1183187	0.0000000	20
Beagle	SUPER	AMR - EUR	0	0.0007263	0.0002884	624.9958	2.5181183	0.0879064	20
Beagle	SUPER	AMR - SAS	0	-0.0023183	0.0003087	624.9958	-7.5100060	0.0000000	20
Beagle	SUPER	EAS - EUR	0	0.0046701	0.0003408	624.9958	13.7036535	0.0000000	20
Beagle	SUPER	EAS - SAS	0	0.0016255	0.0003581	624.9958	4.5392309	0.0000663	20
Beagle	SUPER	EUR - SAS	0	-0.0030446	0.0003248	624.9958	-9.3726940	0.0000000	20
Eagle	SUPER	AFR - AMR	0	-0.0021922	0.0002477	624.9958	-8.8501815	0.0000000	20
Eagle	SUPER	AFR - EAS	0	-0.0063671	0.0003071	624.9958	-20.7348940	0.0000000	20
Eagle	SUPER	AFR - EUR	0	-0.0015824	0.0002676	624.9958	-5.9145031	0.0000001	20
Eagle	SUPER	AFR - SAS	0	-0.0044268	0.0002893	624.9958	-15.3035387	0.0000000	20
Eagle	SUPER	AMR - EAS	0	-0.0041749	0.0003254	624.9958	-12.8286031	0.0000000	20
Eagle	SUPER	AMR - EUR	0	0.0006097	0.0002884	624.9958	2.1138627	0.2153785	20
Eagle	SUPER	AMR - SAS	0	-0.0022346	0.0003087	624.9958	-7.2389551	0.0000000	20
Eagle	SUPER	EAS - EUR	0	0.0047846	0.0003408	624.9958	14.0397749	0.0000000	20
Eagle	SUPER	EAS - SAS	0	0.0019403	0.0003581	624.9958	5.4184029	0.0000009	20
Eagle	SUPER	EUR - SAS	0	-0.0028444	0.0003248	624.9958	-8.7561534	0.0000000	20
SHAPEIT	SUPER	AFR - AMR	0	-0.0019839	0.0002477	624.9958	-8.0095161	0.0000000	20
SHAPEIT	SUPER	AFR - EAS	0	-0.0059898	0.0003071	624.9958	-19.5063328	0.0000000	20
SHAPEIT	SUPER	AFR - EUR	0	-0.0010475	0.0002676	624.9958	-3.9152178	0.0009488	20
SHAPEIT	SUPER	AFR - SAS	0	-0.0043254	0.0002893	624.9958	-14.9529285	0.0000000	20
SHAPEIT	SUPER	AMR - EAS	0	-0.0040059	0.0003254	624.9958	-12.3092271	0.0000000	20
SHAPEIT	SUPER	AMR - EUR	0	0.0009364	0.0002884	624.9958	3.2464170	0.0107676	20
SHAPEIT	SUPER	AMR - SAS	0	-0.0023414	0.0003087	624.9958	-7.5849650	0.0000000	20
SHAPEIT	SUPER	EAS - EUR	0	0.0049423	0.0003408	624.9958	14.5023907	0.0000000	20
SHAPEIT	SUPER	EAS - SAS	0	0.0016645	0.0003581	624.9958	4.6481116	0.0000401	20
SHAPEIT	SUPER	EUR - SAS	0	-0.0032778	0.0003248	624.9958	-10.0906273	0.0000000	20
Beagle	SUPER	AFR - AMR	0	-0.0007372	0.0002263	643.1741	-3.2576924	0.0103616	21
Beagle	SUPER	AFR - EAS	0	-0.0036969	0.0002806	643.1741	-13.1770282	0.0000000	21
Beagle	SUPER	AFR - EUR	0	-0.0003914	0.0002444	643.1741	-1.6011994	0.4971217	21
Beagle	SUPER	AFR - SAS	0	-0.0028476	0.0002643	643.1741	-10.7746926	0.0000000	21
Beagle	SUPER	AMR - EAS	0	-0.0029596	0.0002973	643.1741	-9.9538464	0.0000000	21
Beagle	SUPER	AMR - EUR	0	0.0003458	0.0002635	643.1741	1.3122716	0.6836824	21
Beagle	SUPER	AMR - SAS	0	-0.0021104	0.0002820	643.1741	-7.4825790	0.0000000	21
Beagle	SUPER	EAS - EUR	0	0.0033054	0.0003114	643.1741	10.6160764	0.0000000	21
Beagle	SUPER	EAS - SAS	0	0.0008493	0.0003272	643.1741	2.5957829	0.0723010	21
Beagle	SUPER	EUR - SAS	0	-0.0024562	0.0002968	643.1741	-8.2758864	0.0000000	21
Eagle	SUPER	AFR - AMR	0	-0.0011533	0.0002263	643.1741	-5.0959624	0.0000045	21
Eagle	SUPER	AFR - EAS	0	-0.0042066	0.0002806	643.1741	-14.9940614	0.0000000	21
Eagle	SUPER	AFR - EUR	0	-0.0008309	0.0002444	643.1741	-3.3992532	0.0064259	21
Eagle	SUPER	AFR - SAS	0	-0.0032272	0.0002643	643.1741	-12.2111418	0.0000000	21
Eagle	SUPER	AMR - EAS	0	-0.0030534	0.0002973	643.1741	-10.2691848	0.0000000	21
Eagle	SUPER	AMR - EUR	0	0.0003223	0.0002635	643.1741	1.2230462	0.7379489	21
Eagle	SUPER	AMR - SAS	0	-0.0020740	0.0002820	643.1741	-7.3535865	0.0000000	21
Eagle	SUPER	EAS - EUR	0	0.0033757	0.0003114	643.1741	10.8416870	0.0000000	21
Eagle	SUPER	EAS - SAS	0	0.0009794	0.0003272	643.1741	2.9935632	0.0238569	21
Eagle	SUPER	EUR - SAS	0	-0.0023963	0.0002968	643.1741	-8.0740772	0.0000000	21
SHAPEIT	SUPER	AFR - AMR	0	-0.0008927	0.0002263	643.1741	-3.9446457	0.0008415	21
SHAPEIT	SUPER	AFR - EAS	0	-0.0037265	0.0002806	643.1741	-13.2827307	0.0000000	21
SHAPEIT	SUPER	AFR - EUR	0	-0.0003472	0.0002444	643.1741	-1.4202424	0.6147922	21
SHAPEIT	SUPER	AFR - SAS	0	-0.0030795	0.0002643	643.1741	-11.6520154	0.0000000	21
SHAPEIT	SUPER	AMR - EAS	0	-0.0028338	0.0002973	643.1741	-9.5307290	0.0000000	21
SHAPEIT	SUPER	AMR - EUR	0	0.0005455	0.0002635	643.1741	2.0700286	0.2344216	21
SHAPEIT	SUPER	AMR - SAS	0	-0.0021868	0.0002820	643.1741	-7.7534713	0.0000000	21
SHAPEIT	SUPER	EAS - EUR	0	0.0033793	0.0003114	643.1741	10.8533863	0.0000000	21
SHAPEIT	SUPER	EAS - SAS	0	0.0006471	0.0003272	643.1741	1.9777273	0.2780590	21
SHAPEIT	SUPER	EUR - SAS	0	-0.0027323	0.0002968	643.1741	-9.2061716	0.0000000	21
Beagle	SUPER	AFR - AMR	0	-0.0010292	0.0002758	635.3619	-3.7317389	0.0019300	22
Beagle	SUPER	AFR - EAS	0	-0.0049191	0.0003419	635.3619	-14.3868553	0.0000000	22
Beagle	SUPER	AFR - EUR	0	-0.0006473	0.0002979	635.3619	-2.1726565	0.1914428	22
Beagle	SUPER	AFR - SAS	0	-0.0036761	0.0003221	635.3619	-11.4131038	0.0000000	22
Beagle	SUPER	AMR - EAS	0	-0.0038899	0.0003624	635.3619	-10.7345867	0.0000000	22
Beagle	SUPER	AMR - EUR	0	0.0003820	0.0003212	635.3619	1.1892886	0.7575832	22
Beagle	SUPER	AMR - SAS	0	-0.0026468	0.0003437	635.3619	-7.7004335	0.0000000	22
Beagle	SUPER	EAS - EUR	0	0.0042718	0.0003795	635.3619	11.2575478	0.0000000	22
Beagle	SUPER	EAS - SAS	0	0.0012430	0.0003987	635.3619	3.1175250	0.0162906	22
Beagle	SUPER	EUR - SAS	0	-0.0030288	0.0003617	635.3619	-8.3737080	0.0000000	22
Eagle	SUPER	AFR - AMR	0	-0.0013812	0.0002758	635.3619	-5.0079467	0.0000071	22
Eagle	SUPER	AFR - EAS	0	-0.0055010	0.0003419	635.3619	-16.0887347	0.0000000	22
Eagle	SUPER	AFR - EUR	0	-0.0010241	0.0002979	635.3619	-3.4377523	0.0056263	22
Eagle	SUPER	AFR - SAS	0	-0.0039851	0.0003221	635.3619	-12.3727089	0.0000000	22
Eagle	SUPER	AMR - EAS	0	-0.0041198	0.0003624	635.3619	-11.3690675	0.0000000	22
Eagle	SUPER	AMR - EUR	0	0.0003571	0.0003212	635.3619	1.1117540	0.8003720	22
Eagle	SUPER	AMR - SAS	0	-0.0026039	0.0003437	635.3619	-7.5756091	0.0000000	22
Eagle	SUPER	EAS - EUR	0	0.0044769	0.0003795	635.3619	11.7978168	0.0000000	22
Eagle	SUPER	EAS - SAS	0	0.0015159	0.0003987	635.3619	3.8017516	0.0014768	22
Eagle	SUPER	EUR - SAS	0	-0.0029610	0.0003617	635.3619	-8.1862407	0.0000000	22
SHAPEIT	SUPER	AFR - AMR	0	-0.0011736	0.0002758	635.3619	-4.2550574	0.0002325	22
SHAPEIT	SUPER	AFR - EAS	0	-0.0049986	0.0003419	635.3619	-14.6193366	0.0000000	22
SHAPEIT	SUPER	AFR - EUR	0	-0.0006805	0.0002979	635.3619	-2.2843712	0.1512505	22
SHAPEIT	SUPER	AFR - SAS	0	-0.0039901	0.0003221	635.3619	-12.3882304	0.0000000	22
SHAPEIT	SUPER	AMR - EAS	0	-0.0038250	0.0003624	635.3619	-10.5556388	0.0000000	22
SHAPEIT	SUPER	AMR - EUR	0	0.0004930	0.0003212	635.3619	1.5350562	0.5399803	22
SHAPEIT	SUPER	AMR - SAS	0	-0.0028166	0.0003437	635.3619	-8.1942754	0.0000000	22
SHAPEIT	SUPER	EAS - EUR	0	0.0043180	0.0003795	635.3619	11.3793193	0.0000000	22
SHAPEIT	SUPER	EAS - SAS	0	0.0010085	0.0003987	635.3619	2.5291789	0.0855157	22
SHAPEIT	SUPER	EUR - SAS	0	-0.0033096	0.0003617	635.3619	-9.1500304	0.0000000	22
Beagle	SUPER	AFR - AMR	0	-0.0004255	0.0000910	1048.8670	-4.6761548	0.0000325	23
Beagle	SUPER	AFR - EAS	0	-0.0028946	0.0000910	1048.8670	-31.8102658	0.0000000	23
Beagle	SUPER	AFR - EUR	0	-0.0008571	0.0000910	1048.8670	-9.4193721	0.0000000	23
Beagle	SUPER	AFR - SAS	0	-0.0017394	0.0000910	1048.8670	-19.1148049	0.0000000	23
Beagle	SUPER	AMR - EAS	0	-0.0024691	0.0000910	1048.8670	-27.1341110	0.0000000	23
Beagle	SUPER	AMR - EUR	0	-0.0004316	0.0000910	1048.8670	-4.7432172	0.0000236	23
Beagle	SUPER	AMR - SAS	0	-0.0013139	0.0000910	1048.8670	-14.4386500	0.0000000	23
Beagle	SUPER	EAS - EUR	0	0.0020375	0.0000910	1048.8670	22.3908937	0.0000000	23
Beagle	SUPER	EAS - SAS	0	0.0011552	0.0000910	1048.8670	12.6954609	0.0000000	23
Beagle	SUPER	EUR - SAS	0	-0.0008822	0.0000910	1048.8670	-9.6954328	0.0000000	23
Eagle	SUPER	AFR - AMR	0	-0.0004013	0.0000910	1048.8670	-4.4099380	0.0001112	23
Eagle	SUPER	AFR - EAS	0	-0.0032492	0.0000910	1048.8670	-35.7067602	0.0000000	23
Eagle	SUPER	AFR - EUR	0	-0.0009391	0.0000910	1048.8670	-10.3203979	0.0000000	23
Eagle	SUPER	AFR - SAS	0	-0.0019586	0.0000910	1048.8670	-21.5237585	0.0000000	23
Eagle	SUPER	AMR - EAS	0	-0.0028479	0.0000910	1048.8670	-31.2968222	0.0000000	23
Eagle	SUPER	AMR - EUR	0	-0.0005378	0.0000910	1048.8670	-5.9104599	0.0000000	23
Eagle	SUPER	AMR - SAS	0	-0.0015573	0.0000910	1048.8670	-17.1138205	0.0000000	23
Eagle	SUPER	EAS - EUR	0	0.0023101	0.0000910	1048.8670	25.3863622	0.0000000	23
Eagle	SUPER	EAS - SAS	0	0.0012906	0.0000910	1048.8670	14.1830017	0.0000000	23
Eagle	SUPER	EUR - SAS	0	-0.0010195	0.0000910	1048.8670	-11.2033606	0.0000000	23
SHAPEIT	SUPER	AFR - AMR	0	-0.0004491	0.0000910	1048.8670	-4.9351372	0.0000092	23
SHAPEIT	SUPER	AFR - EAS	0	-0.0027998	0.0000910	1048.8670	-30.7685457	0.0000000	23
SHAPEIT	SUPER	AFR - EUR	0	-0.0008528	0.0000910	1048.8670	-9.3721252	0.0000000	23
SHAPEIT	SUPER	AFR - SAS	0	-0.0016975	0.0000910	1048.8670	-18.6541676	0.0000000	23
SHAPEIT	SUPER	AMR - EAS	0	-0.0023507	0.0000910	1048.8670	-25.8334085	0.0000000	23
SHAPEIT	SUPER	AMR - EUR	0	-0.0004037	0.0000910	1048.8670	-4.4369880	0.0000984	23
SHAPEIT	SUPER	AMR - SAS	0	-0.0012484	0.0000910	1048.8670	-13.7190304	0.0000000	23
SHAPEIT	SUPER	EAS - EUR	0	0.0019470	0.0000910	1048.8670	21.3964205	0.0000000	23
SHAPEIT	SUPER	EAS - SAS	0	0.0011024	0.0000910	1048.8670	12.1143781	0.0000000	23
SHAPEIT	SUPER	EUR - SAS	0	-0.0008446	0.0000910	1048.8670	-9.2820424	0.0000000	23

Switch Errors

Next, let’s consider switches and flips independently:

# df_switches <- df_switch_trio[[1]] %>%
#   mutate(Eagle = (n_other_eagle) / n_hets,
#          Beagle = (n_other_beagle) / n_hets,
#          SHAPEIT = (n_other_shapeit) / n_hets) %>%
#   select(Eagle, Beagle, SHAPEIT, SUPER, pair_id) %>%
#   mutate(chrom = 1)
# 
# for(i in 2:22){
#   df_switches <- bind_rows(df_switches, 
#                         {
#                           df_switch_trio[[i]] %>%
#                             mutate(Eagle = (n_other_eagle) / n_hets,
#                                    Beagle = (n_other_beagle) / n_hets,
#                                    SHAPEIT = (n_other_shapeit) / n_hets) %>%
#                             select(Eagle, Beagle, SHAPEIT, SUPER, pair_id) %>%
#                             mutate(chrom = i)
#                         })
# }
# 


df_switches <- df_switch_trio_noth %>%
  mutate(Eagle = (n_switch_e) / n_het,
         Beagle = (n_switch_b) / n_het,
         SHAPEIT = (n_switch_s) / n_het) %>%
  select(Eagle, Beagle, SHAPEIT, sample, chrom)

df_switches <- df_switches %>%
  left_join({df_subj_rel %>% select(id2, SUPER)}, by = c("sample" = "id2")) %>%
  rename(pair_id = sample) %>%
  select(Eagle, Beagle, SHAPEIT, SUPER, pair_id, chrom)

df_switches <- df_switches %>%
  bind_rows({df_switch_x %>%
      mutate(Eagle = (n_other_eagle) / n_hets,
                                   Beagle = (n_other_beagle) / n_hets,
                                   SHAPEIT = (n_other_shapeit) / n_hets) %>%
      rename(SUPER = pop) %>%
                            select(Eagle, Beagle, SHAPEIT, SUPER) %>%
                            mutate(pair_id = 603:1602, chrom = 23)})

df_switches %>%
  group_by(chrom) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>%
  knitr::kable()

chrom	Beagle	Eagle	SHAPEIT
1	0.0019084	0.0024999	0.0018737
2	0.0017862	0.0023895	0.0017640
3	0.0016596	0.0022318	0.0016561
4	0.0015058	0.0020500	0.0014972
5	0.0016545	0.0022052	0.0016464
6	0.0014645	0.0019622	0.0014465
7	0.0018935	0.0024565	0.0018503
8	0.0016766	0.0022457	0.0016720
9	0.0025877	0.0031912	0.0025272
10	0.0018561	0.0024419	0.0018115
11	0.0017216	0.0023083	0.0016987
12	0.0018425	0.0024028	0.0018366
13	0.0017893	0.0023635	0.0017801
14	0.0021114	0.0027364	0.0021083
15	0.0027363	0.0034055	0.0027022
16	0.0025976	0.0033503	0.0025877
17	0.0027715	0.0035106	0.0027148
18	0.0020664	0.0026810	0.0020536
19	0.0027082	0.0033871	0.0026400
20	0.0027694	0.0034397	0.0026885
21	0.0032355	0.0038173	0.0032186
22	0.0038186	0.0045225	0.0036899
23	0.0017000	0.0022896	0.0015654

df_switches %>%
  group_by(chrom, SUPER) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>%  
  knitr::kable() 

`summarise()` has grouped output by 'chrom'. You can override using the
`.groups` argument.

chrom	SUPER	Beagle	Eagle	SHAPEIT
1	AFR	0.0013031	0.0017879	0.0012370
1	AMR	0.0017838	0.0023339	0.0017660
1	EAS	0.0031973	0.0041090	0.0032297
1	EUR	0.0017845	0.0023154	0.0017281
1	SAS	0.0026048	0.0033203	0.0025879
2	AFR	0.0012032	0.0017167	0.0011570
2	AMR	0.0017330	0.0023111	0.0017309
2	EAS	0.0030258	0.0038904	0.0030452
2	EUR	0.0015921	0.0021094	0.0015504
2	SAS	0.0024448	0.0031883	0.0024363
3	AFR	0.0011096	0.0016027	0.0010764
3	AMR	0.0015866	0.0021087	0.0015880
3	EAS	0.0027729	0.0036531	0.0028329
3	EUR	0.0015385	0.0020425	0.0015186
3	SAS	0.0022871	0.0029521	0.0023130
4	AFR	0.0009938	0.0014277	0.0009428
4	AMR	0.0015003	0.0020231	0.0015086
4	EAS	0.0024240	0.0032640	0.0025213
4	EUR	0.0013769	0.0018891	0.0013453
4	SAS	0.0021102	0.0027394	0.0021138
5	AFR	0.0010981	0.0015620	0.0010441
5	AMR	0.0015576	0.0020605	0.0016006
5	EAS	0.0027997	0.0036286	0.0028362
5	EUR	0.0015035	0.0020003	0.0014763
5	SAS	0.0023465	0.0030116	0.0023506
6	AFR	0.0010003	0.0014310	0.0009608
6	AMR	0.0013976	0.0018431	0.0013981
6	EAS	0.0024011	0.0031797	0.0024318
6	EUR	0.0013123	0.0017258	0.0012665
6	SAS	0.0020679	0.0026763	0.0020650
7	AFR	0.0013913	0.0018807	0.0013021
7	AMR	0.0017797	0.0022894	0.0017757
7	EAS	0.0030445	0.0038232	0.0030652
7	EUR	0.0017074	0.0022170	0.0016397
7	SAS	0.0025239	0.0032315	0.0025031
8	AFR	0.0010952	0.0015763	0.0010574
8	AMR	0.0016408	0.0021809	0.0016906
8	EAS	0.0028758	0.0037101	0.0028902
8	EUR	0.0015261	0.0020471	0.0015018
8	SAS	0.0022823	0.0029429	0.0022780
9	AFR	0.0019710	0.0024755	0.0018571
9	AMR	0.0023622	0.0029090	0.0023513
9	EAS	0.0039947	0.0049926	0.0040020
9	EUR	0.0024834	0.0030163	0.0024100
9	SAS	0.0033491	0.0040325	0.0032937
10	AFR	0.0013054	0.0018014	0.0012220
10	AMR	0.0017613	0.0023007	0.0017395
10	EAS	0.0029666	0.0038215	0.0030032
10	EUR	0.0017012	0.0022140	0.0016233
10	SAS	0.0025656	0.0033022	0.0025487
11	AFR	0.0011327	0.0016113	0.0010900
11	AMR	0.0016660	0.0022169	0.0016743
11	EAS	0.0028719	0.0037021	0.0028828
11	EUR	0.0015605	0.0021015	0.0015069
11	SAS	0.0024324	0.0031835	0.0024156
12	AFR	0.0012347	0.0016935	0.0011711
12	AMR	0.0017109	0.0022619	0.0017431
12	EAS	0.0030297	0.0038845	0.0030974
12	EUR	0.0016848	0.0022047	0.0016367
12	SAS	0.0026850	0.0033016	0.0027443
13	AFR	0.0012374	0.0016608	0.0011887
13	AMR	0.0016338	0.0021985	0.0016718
13	EAS	0.0030470	0.0038889	0.0030357
13	EUR	0.0016449	0.0021782	0.0016133
13	SAS	0.0024617	0.0032325	0.0024994
14	AFR	0.0015135	0.0020048	0.0014646
14	AMR	0.0020288	0.0026707	0.0020724
14	EAS	0.0033255	0.0042777	0.0033896
14	EUR	0.0019515	0.0025040	0.0019100
14	SAS	0.0028314	0.0035589	0.0028525
15	AFR	0.0020558	0.0026301	0.0019531
15	AMR	0.0024911	0.0031218	0.0025112
15	EAS	0.0042257	0.0051794	0.0042498
15	EUR	0.0026587	0.0032128	0.0025716
15	SAS	0.0035765	0.0044363	0.0036347
16	AFR	0.0018445	0.0025092	0.0017355
16	AMR	0.0024940	0.0031937	0.0025249
16	EAS	0.0041844	0.0052628	0.0042751
16	EUR	0.0023658	0.0031430	0.0024116
16	SAS	0.0034933	0.0042329	0.0034969
17	AFR	0.0019400	0.0025814	0.0018683
17	AMR	0.0025915	0.0032833	0.0025548
17	EAS	0.0045569	0.0055374	0.0046059
17	EUR	0.0025843	0.0032542	0.0025085
17	SAS	0.0037514	0.0046797	0.0036319
18	AFR	0.0013736	0.0018761	0.0013308
18	AMR	0.0019493	0.0025107	0.0019493
18	EAS	0.0034908	0.0044029	0.0035391
18	EUR	0.0019470	0.0025446	0.0019378
18	SAS	0.0028371	0.0035722	0.0028183
19	AFR	0.0019787	0.0026070	0.0018653
19	AMR	0.0025439	0.0031896	0.0024700
19	EAS	0.0043873	0.0053070	0.0043948
19	EUR	0.0025013	0.0031173	0.0024208
19	SAS	0.0035366	0.0042639	0.0035355
20	AFR	0.0019127	0.0025023	0.0017881
20	AMR	0.0026849	0.0033720	0.0026430
20	EAS	0.0046822	0.0055716	0.0046542
20	EUR	0.0025032	0.0030775	0.0024023
20	SAS	0.0036461	0.0044155	0.0035863
21	AFR	0.0027883	0.0032811	0.0027103
21	AMR	0.0030047	0.0035338	0.0030654
21	EAS	0.0044825	0.0052999	0.0044698
21	EUR	0.0029705	0.0035425	0.0029284
21	SAS	0.0039422	0.0046324	0.0039729
22	AFR	0.0030976	0.0037686	0.0028908
22	AMR	0.0035044	0.0041885	0.0034282
22	EAS	0.0056296	0.0065746	0.0054882
22	EUR	0.0035995	0.0041890	0.0035406
22	SAS	0.0047719	0.0055252	0.0046662
23	AFR	0.0008880	0.0013558	0.0007707
23	AMR	0.0012206	0.0016760	0.0011439
23	EAS	0.0028352	0.0036614	0.0026536
23	EUR	0.0015108	0.0020636	0.0013951
23	SAS	0.0020451	0.0026914	0.0018639

df_switches %>%
  group_by(chrom) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>%
  pivot_longer(Beagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  ggplot(aes(x = chrom, y = error_rate, colour = method, shape = method)) +
  geom_point(size=3) +
  theme_bw() +
  xlab("Chromosome") +
  ylab("Switch Rate") +
  labs(colour = "Method", shape = "Method") +
  scale_colour_brewer(palette = "Set2") +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5)) +
  scale_x_continuous("Chromosome", labels = as.character(unique(df_switches$chrom)), breaks = unique(df_switches$chrom))

Past versions of unnamed-chunk-18-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
17d41d5	Andy Beck	2024-05-22
d7d8f5a	Andy Beck	2024-05-22
da672c2	Andy Beck	2024-05-22

df_switches %>%
  group_by(chrom, SUPER) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>%
  pivot_longer(Beagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  ggplot(aes(x = chrom, y = error_rate, colour = SUPER, shape = method)) +
  geom_point(size=2) +
  theme_bw() +
  ylab("Switch Rate") +
  xlab("Chromosome") +
  labs(colour = "Population", shape = "Method") +
  scale_colour_brewer(palette = "Set1") +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5)) +
  scale_x_continuous("Chromosome", labels = as.character(unique(df_switches$chrom)), breaks = unique(df_switches$chrom))

`summarise()` has grouped output by 'chrom'. You can override using the
`.groups` argument.

Past versions of unnamed-chunk-18-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
17d41d5	Andy Beck	2024-05-22
d7d8f5a	Andy Beck	2024-05-22
da672c2	Andy Beck	2024-05-22

mod_b <- df_switches %>%
  select(Beagle, Eagle, SHAPEIT, chrom, pair_id) %>%
  {lmerTest::lmer(Beagle ~ factor(chrom) + (1|pair_id), data = . )}
anova(mod_b) %>% broom::tidy()

# A tibble: 1 × 7
  term            sumsq   meansq NumDF DenDF statistic p.value
  <chr>           <dbl>    <dbl> <int> <dbl>     <dbl>   <dbl>
1 factor(chrom) 0.00490 0.000223    22 9521.     1092.       0

emmeans::emmeans(mod_b, ~ chrom, pbkrtest.limit = 14244) %>% pairs() %>% broom::tidy() %>%
  separate(contrast, into = c("chrom1", "chrom2"), sep = " - ") %>%
  filter(chrom1 %in% "chrom23" | chrom2 %in% "chrom23") %>% 
  knitr::kable()

term	chrom1	chrom2	null.value	estimate	std.error	df	statistic	adj.p.value
chrom	chrom1	chrom23	0	0.0002085	4.79e-05	1997.721	4.3518930	0.0030782
chrom	chrom2	chrom23	0	0.0000862	4.79e-05	1997.721	1.8000017	0.9797694
chrom	chrom3	chrom23	0	-0.0000404	4.79e-05	1997.721	-0.8433140	0.9999999
chrom	chrom4	chrom23	0	-0.0001941	4.79e-05	1997.721	-4.0528337	0.0105070
chrom	chrom5	chrom23	0	-0.0000454	4.79e-05	1997.721	-0.9487342	0.9999991
chrom	chrom6	chrom23	0	-0.0002355	4.79e-05	1997.721	-4.9167873	0.0002260
chrom	chrom7	chrom23	0	0.0001936	4.79e-05	1997.721	4.0408783	0.0110090
chrom	chrom8	chrom23	0	-0.0000234	4.79e-05	1997.721	-0.4886566	1.0000000
chrom	chrom9	chrom23	0	0.0008878	4.79e-05	1997.721	18.5333599	0.0000000
chrom	chrom10	chrom23	0	0.0001561	4.79e-05	1997.721	3.2595434	0.1477995
chrom	chrom11	chrom23	0	0.0000217	4.79e-05	1997.721	0.4521216	1.0000000
chrom	chrom12	chrom23	0	0.0001425	4.79e-05	1997.721	2.9758272	0.2947120
chrom	chrom13	chrom23	0	0.0000894	4.79e-05	1997.721	1.8659699	0.9696929
chrom	chrom14	chrom23	0	0.0004115	4.79e-05	1997.721	8.5899605	0.0000000
chrom	chrom15	chrom23	0	0.0010363	4.79e-05	1997.721	21.6344847	0.0000000
chrom	chrom16	chrom23	0	0.0008977	4.79e-05	1997.721	18.7400917	0.0000000
chrom	chrom17	chrom23	0	0.0010716	4.79e-05	1997.721	22.3708948	0.0000000
chrom	chrom18	chrom23	0	0.0003664	4.79e-05	1997.721	7.6499754	0.0000000
chrom	chrom19	chrom23	0	0.0010083	4.79e-05	1997.721	21.0494934	0.0000000
chrom	chrom20	chrom23	0	0.0010694	4.79e-05	1997.721	22.3259912	0.0000000
chrom	chrom21	chrom23	0	0.0015355	4.79e-05	1997.721	32.0565019	0.0000000
chrom	chrom22	chrom23	0	0.0021187	4.79e-05	1997.721	44.2305362	0.0000000

mod_e <- df_switches %>%
  select(Beagle, Eagle, SHAPEIT, chrom, pair_id) %>%
  {lmerTest::lmer(Eagle ~ factor(chrom) + (1|pair_id), data = . )}
anova(mod_e) %>% broom::tidy()

# A tibble: 1 × 7
  term            sumsq   meansq NumDF DenDF statistic p.value
  <chr>           <dbl>    <dbl> <int> <dbl>     <dbl>   <dbl>
1 factor(chrom) 0.00571 0.000259    22 9467.     1191.       0

emmeans::emmeans(mod_e, ~ chrom, pbkrtest.limit = 14244) %>% pairs() %>% broom::tidy() %>%
  separate(contrast, into = c("chrom1", "chrom2"), sep = " - ") %>%
  filter(chrom1 %in% "chrom23" | chrom2 %in% "chrom23") %>% 
  knitr::kable()

term	chrom1	chrom2	null.value	estimate	std.error	df	statistic	adj.p.value
chrom	chrom1	chrom23	0	0.0002103	5.47e-05	1900.994	3.8420012	0.0232835
chrom	chrom2	chrom23	0	0.0000999	5.47e-05	1900.994	1.8253984	0.9762487
chrom	chrom3	chrom23	0	-0.0000578	5.47e-05	1900.994	-1.0567801	0.9999933
chrom	chrom4	chrom23	0	-0.0002396	5.47e-05	1900.994	-4.3775428	0.0027624
chrom	chrom5	chrom23	0	-0.0000844	5.47e-05	1900.994	-1.5426689	0.9971521
chrom	chrom6	chrom23	0	-0.0003275	5.47e-05	1900.994	-5.9834024	0.0000007
chrom	chrom7	chrom23	0	0.0001669	5.47e-05	1900.994	3.0495519	0.2500202
chrom	chrom8	chrom23	0	-0.0000439	5.47e-05	1900.994	-0.8019284	1.0000000
chrom	chrom9	chrom23	0	0.0009016	5.47e-05	1900.994	16.4729705	0.0000000
chrom	chrom10	chrom23	0	0.0001523	5.47e-05	1900.994	2.7819346	0.4316661
chrom	chrom11	chrom23	0	0.0000187	5.47e-05	1900.994	0.3407932	1.0000000
chrom	chrom12	chrom23	0	0.0001132	5.47e-05	1900.994	2.0684998	0.9146935
chrom	chrom13	chrom23	0	0.0000739	5.47e-05	1900.994	1.3500220	0.9995989
chrom	chrom14	chrom23	0	0.0004467	5.47e-05	1900.994	8.1626972	0.0000000
chrom	chrom15	chrom23	0	0.0011159	5.47e-05	1900.994	20.3887982	0.0000000
chrom	chrom16	chrom23	0	0.0010607	5.47e-05	1900.994	19.3807543	0.0000000
chrom	chrom17	chrom23	0	0.0012209	5.47e-05	1900.994	22.3084662	0.0000000
chrom	chrom18	chrom23	0	0.0003914	5.47e-05	1900.994	7.1510578	0.0000000
chrom	chrom19	chrom23	0	0.0010975	5.47e-05	1900.994	20.0531651	0.0000000
chrom	chrom20	chrom23	0	0.0011501	5.47e-05	1900.994	21.0134809	0.0000000
chrom	chrom21	chrom23	0	0.0015277	5.47e-05	1900.994	27.9130811	0.0000000
chrom	chrom22	chrom23	0	0.0022329	5.47e-05	1900.994	40.7981837	0.0000000

mod_s <- df_switches %>%
  select(Beagle, Eagle, SHAPEIT, chrom, pair_id) %>%
  {lmerTest::lmer(SHAPEIT ~ factor(chrom) + (1|pair_id), data = . )}
anova(mod_s) %>% broom::tidy()

# A tibble: 1 × 7
  term            sumsq   meansq NumDF DenDF statistic p.value
  <chr>           <dbl>    <dbl> <int> <dbl>     <dbl>   <dbl>
1 factor(chrom) 0.00457 0.000208    22 9600.      931.       0

emmeans::emmeans(mod_s, ~ chrom, pbkrtest.limit = 14244) %>% pairs() %>% broom::tidy() %>%
  separate(contrast, into = c("chrom1", "chrom2"), sep = " - ") %>%
  filter(chrom1 %in% "chrom23" | chrom2 %in% "chrom23") %>% 
  knitr::kable()

term	chrom1	chrom2	null.value	estimate	std.error	df	statistic	adj.p.value
chrom	chrom1	chrom23	0	0.0003083	4.84e-05	2038.425	6.364209	0.0000001
chrom	chrom2	chrom23	0	0.0001986	4.84e-05	2038.425	4.098871	0.0087573
chrom	chrom3	chrom23	0	0.0000907	4.84e-05	2038.425	1.871582	0.9686901
chrom	chrom4	chrom23	0	-0.0000682	4.84e-05	2038.425	-1.408091	0.9992386
chrom	chrom5	chrom23	0	0.0000810	4.84e-05	2038.425	1.671210	0.9917721
chrom	chrom6	chrom23	0	-0.0001189	4.84e-05	2038.425	-2.455000	0.6892273
chrom	chrom7	chrom23	0	0.0002849	4.84e-05	2038.425	5.880450	0.0000012
chrom	chrom8	chrom23	0	0.0001066	4.84e-05	2038.425	2.200602	0.8551050
chrom	chrom9	chrom23	0	0.0009618	4.84e-05	2038.425	19.852729	0.0000000
chrom	chrom10	chrom23	0	0.0002460	4.84e-05	2038.425	5.078894	0.0000999
chrom	chrom11	chrom23	0	0.0001332	4.84e-05	2038.425	2.750074	0.4561909
chrom	chrom12	chrom23	0	0.0002711	4.84e-05	2038.425	5.596499	0.0000062
chrom	chrom13	chrom23	0	0.0002147	4.84e-05	2038.425	4.430895	0.0021825
chrom	chrom14	chrom23	0	0.0005428	4.84e-05	2038.425	11.205324	0.0000000
chrom	chrom15	chrom23	0	0.0011367	4.84e-05	2038.425	23.464421	0.0000000
chrom	chrom16	chrom23	0	0.0010223	4.84e-05	2038.425	21.102187	0.0000000
chrom	chrom17	chrom23	0	0.0011493	4.84e-05	2038.425	23.724210	0.0000000
chrom	chrom18	chrom23	0	0.0004882	4.84e-05	2038.425	10.076293	0.0000000
chrom	chrom19	chrom23	0	0.0010746	4.84e-05	2038.425	22.180865	0.0000000
chrom	chrom20	chrom23	0	0.0011231	4.84e-05	2038.425	23.182437	0.0000000
chrom	chrom21	chrom23	0	0.0016532	4.84e-05	2038.425	34.124483	0.0000000
chrom	chrom22	chrom23	0	0.0021245	4.84e-05	2038.425	43.853271	0.0000000

# Beagle
autosomes <- df_switches %>%  filter(chrom < 23) %>% pull(Beagle)
chrX <- df_switches %>% filter(chrom == 23) %>% pull(Beagle)
t.test(autosomes, chrX) %>% broom::tidy()

# A tibble: 1 × 10
  estimate estimate1 estimate2 statistic  p.value parameter conf.low conf.high
     <dbl>     <dbl>     <dbl>     <dbl>    <dbl>     <dbl>    <dbl>     <dbl>
1 0.000489   0.00219   0.00170      16.5 1.96e-55     1266. 0.000431  0.000547
# ℹ 2 more variables: method <chr>, alternative <chr>

# Eagle
autosomes <- df_switches %>% filter(chrom < 23) %>% pull(Eagle)
chrX <- df_switches %>% filter(chrom == 23) %>% pull(Eagle)
t.test(autosomes, chrX) %>% broom::tidy()

# A tibble: 1 × 10
  estimate estimate1 estimate2 statistic  p.value parameter conf.low conf.high
     <dbl>     <dbl>     <dbl>     <dbl>    <dbl>     <dbl>    <dbl>     <dbl>
1 0.000510   0.00280   0.00229      14.7 5.10e-45     1230. 0.000442  0.000579
# ℹ 2 more variables: method <chr>, alternative <chr>

# SHAPEIT
autosomes <- df_switches %>% filter(chrom < 23) %>% pull(SHAPEIT)
chrX <- df_switches %>% filter(chrom == 23) %>% pull(SHAPEIT)
t.test(autosomes, chrX) %>% broom::tidy()

# A tibble: 1 × 10
  estimate estimate1 estimate2 statistic  p.value parameter conf.low conf.high
     <dbl>     <dbl>     <dbl>     <dbl>    <dbl>     <dbl>    <dbl>     <dbl>
1 0.000592   0.00216   0.00157      20.4 1.43e-80     1295. 0.000535  0.000649
# ℹ 2 more variables: method <chr>, alternative <chr>

mod_fit <- df_switches %>%
  filter(chrom == 1) %>%
  pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  {lmerTest::lmer(error_rate ~ method + (1|pair_id), data = .)}

df_anova <- anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = 1)

df_pairwise <- emmeans::emmeans(mod_fit, ~ method) %>% pairs() %>% broom::tidy() %>% mutate(chrom=1)

for(i in 2:23){
  mod_fit <- df_switches %>%
    filter(chrom == i) %>%
    pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
    {lmerTest::lmer(error_rate ~ method + (1|pair_id), data = .)}
  
  df_anova <- df_anova %>% bind_rows({anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = i)})
  df_pairwise <- df_pairwise %>% bind_rows({
    emmeans::emmeans(mod_fit, ~ method) %>% pairs() %>% broom::tidy() %>% mutate(chrom=i)})
}

df_anova %>% knitr::kable()

term	sumsq	meansq	NumDF	DenDF	statistic	p.value	chrom
method	0.0001491	0.0000746	2	1202	3681.9647	0	1
method	0.0001517	0.0000758	2	1202	4198.5629	0	2
method	0.0001322	0.0000661	2	1202	3641.1256	0	3
method	0.0001208	0.0000604	2	1202	3592.7161	0	4
method	0.0001235	0.0000618	2	1202	3082.7573	0	5
method	0.0001031	0.0000516	2	1202	2828.8144	0	6
method	0.0001377	0.0000689	2	1202	3275.4743	0	7
method	0.0001311	0.0000655	2	1202	2834.3344	0	8
method	0.0001623	0.0000811	2	1202	2145.1325	0	9
method	0.0001490	0.0000745	2	1202	3192.6028	0	10
method	0.0001437	0.0000719	2	1202	2794.6550	0	11
method	0.0001274	0.0000637	2	1202	1211.4197	0	12
method	0.0001345	0.0000672	2	1202	1955.5305	0	13
method	0.0001575	0.0000788	2	1202	2029.5949	0	14
method	0.0001894	0.0000947	2	1202	1776.8041	0	15
method	0.0002304	0.0001152	2	1202	2021.3109	0	16
method	0.0002373	0.0001187	2	1202	2081.4072	0	17
method	0.0001548	0.0000774	2	1202	1772.8476	0	18
method	0.0002054	0.0001027	2	1202	1771.9228	0	19
method	0.0002047	0.0001024	2	1202	1744.3432	0	20
method	0.0001399	0.0000700	2	1202	761.6489	0	21
method	0.0002418	0.0001209	2	1202	963.2671	0	22
method	0.0002968	0.0001484	2	1998	4651.3018	0	23

df_pairwise %>% knitr::kable()

term	contrast	null.value	estimate	std.error	df	statistic	adj.p.value	chrom
method	Beagle - Eagle	0	-0.0005915	8.20e-06	1202	-72.1124435	0.0000000	1
method	Beagle - SHAPEIT	0	0.0000347	8.20e-06	1202	4.2276912	0.0000753	1
method	Eagle - SHAPEIT	0	0.0006262	8.20e-06	1202	76.3401347	0.0000000	1
method	Beagle - Eagle	0	-0.0006033	7.70e-06	1202	-77.8881980	0.0000000	2
method	Beagle - SHAPEIT	0	0.0000222	7.70e-06	1202	2.8639849	0.0118423	2
method	Eagle - SHAPEIT	0	0.0006255	7.70e-06	1202	80.7521829	0.0000000	2
method	Beagle - Eagle	0	-0.0005722	7.80e-06	1202	-73.6787080	0.0000000	3
method	Beagle - SHAPEIT	0	0.0000035	7.80e-06	1202	0.4470285	0.8957285	3
method	Eagle - SHAPEIT	0	0.0005757	7.80e-06	1202	74.1257365	0.0000000	3
method	Beagle - Eagle	0	-0.0005442	7.50e-06	1202	-72.8267201	0.0000000	4
method	Beagle - SHAPEIT	0	0.0000086	7.50e-06	1202	1.1535897	0.4813231	4
method	Eagle - SHAPEIT	0	0.0005528	7.50e-06	1202	73.9803098	0.0000000	4
method	Beagle - Eagle	0	-0.0005507	8.20e-06	1202	-67.4973130	0.0000000	5
method	Beagle - SHAPEIT	0	0.0000081	8.20e-06	1202	0.9964217	0.5792582	5
method	Eagle - SHAPEIT	0	0.0005588	8.20e-06	1202	68.4937347	0.0000000	5
method	Beagle - Eagle	0	-0.0004977	7.80e-06	1202	-63.9557532	0.0000000	6
method	Beagle - SHAPEIT	0	0.0000180	7.80e-06	1202	2.3072203	0.0551773	6
method	Eagle - SHAPEIT	0	0.0005157	7.80e-06	1202	66.2629735	0.0000000	6
method	Beagle - Eagle	0	-0.0005630	8.40e-06	1202	-67.3657237	0.0000000	7
method	Beagle - SHAPEIT	0	0.0000432	8.40e-06	1202	5.1707846	0.0000008	7
method	Eagle - SHAPEIT	0	0.0006062	8.40e-06	1202	72.5365082	0.0000000	7
method	Beagle - Eagle	0	-0.0005692	8.80e-06	1202	-64.9441124	0.0000000	8
method	Beagle - SHAPEIT	0	0.0000045	8.80e-06	1202	0.5157943	0.8636589	8
method	Eagle - SHAPEIT	0	0.0005737	8.80e-06	1202	65.4599067	0.0000000	8
method	Beagle - Eagle	0	-0.0006035	1.12e-05	1202	-53.8327217	0.0000000	9
method	Beagle - SHAPEIT	0	0.0000605	1.12e-05	1202	5.3981457	0.0000002	9
method	Eagle - SHAPEIT	0	0.0006640	1.12e-05	1202	59.2308674	0.0000000	9
method	Beagle - Eagle	0	-0.0005858	8.80e-06	1202	-66.5288037	0.0000000	10
method	Beagle - SHAPEIT	0	0.0000446	8.80e-06	1202	5.0676065	0.0000014	10
method	Eagle - SHAPEIT	0	0.0006304	8.80e-06	1202	71.5964102	0.0000000	10
method	Beagle - Eagle	0	-0.0005867	9.20e-06	1202	-63.4675437	0.0000000	11
method	Beagle - SHAPEIT	0	0.0000230	9.20e-06	1202	2.4844345	0.0349814	11
method	Eagle - SHAPEIT	0	0.0006096	9.20e-06	1202	65.9519782	0.0000000	11
method	Beagle - Eagle	0	-0.0005603	1.32e-05	1202	-42.4007339	0.0000000	12
method	Beagle - SHAPEIT	0	0.0000060	1.32e-05	1202	0.4505651	0.8941638	12
method	Eagle - SHAPEIT	0	0.0005663	1.32e-05	1202	42.8512989	0.0000000	12
method	Beagle - Eagle	0	-0.0005742	1.07e-05	1202	-53.7215046	0.0000000	13
method	Beagle - SHAPEIT	0	0.0000093	1.07e-05	1202	0.8664128	0.6616136	13
method	Eagle - SHAPEIT	0	0.0005834	1.07e-05	1202	54.5879174	0.0000000	13
method	Beagle - Eagle	0	-0.0006249	1.14e-05	1202	-55.0367662	0.0000000	14
method	Beagle - SHAPEIT	0	0.0000032	1.14e-05	1202	0.2774466	0.9584566	14
method	Eagle - SHAPEIT	0	0.0006281	1.14e-05	1202	55.3142128	0.0000000	14
method	Beagle - Eagle	0	-0.0006692	1.33e-05	1202	-50.2969730	0.0000000	15
method	Beagle - SHAPEIT	0	0.0000341	1.33e-05	1202	2.5619267	0.0283741	15
method	Eagle - SHAPEIT	0	0.0007033	1.33e-05	1202	52.8588996	0.0000000	15
method	Beagle - Eagle	0	-0.0007527	1.38e-05	1202	-54.7005693	0.0000000	16
method	Beagle - SHAPEIT	0	0.0000099	1.38e-05	1202	0.7184190	0.7526318	16
method	Eagle - SHAPEIT	0	0.0007626	1.38e-05	1202	55.4189884	0.0000000	16
method	Beagle - Eagle	0	-0.0007390	1.38e-05	1202	-53.6987663	0.0000000	17
method	Beagle - SHAPEIT	0	0.0000568	1.38e-05	1202	4.1254878	0.0001170	17
method	Eagle - SHAPEIT	0	0.0007958	1.38e-05	1202	57.8242541	0.0000000	17
method	Beagle - Eagle	0	-0.0006146	1.20e-05	1202	-51.0276338	0.0000000	18
method	Beagle - SHAPEIT	0	0.0000128	1.20e-05	1202	1.0644983	0.5363635	18
method	Eagle - SHAPEIT	0	0.0006274	1.20e-05	1202	52.0921321	0.0000000	18
method	Beagle - Eagle	0	-0.0006789	1.39e-05	1202	-48.9194865	0.0000000	19
method	Beagle - SHAPEIT	0	0.0000682	1.39e-05	1202	4.9179190	0.0000030	19
method	Eagle - SHAPEIT	0	0.0007471	1.39e-05	1202	53.8374055	0.0000000	19
method	Beagle - Eagle	0	-0.0006703	1.40e-05	1202	-48.0091624	0.0000000	20
method	Beagle - SHAPEIT	0	0.0000809	1.40e-05	1202	5.7923147	0.0000000	20
method	Eagle - SHAPEIT	0	0.0007512	1.40e-05	1202	53.8014771	0.0000000	20
method	Beagle - Eagle	0	-0.0005818	1.75e-05	1202	-33.3071614	0.0000000	21
method	Beagle - SHAPEIT	0	0.0000169	1.75e-05	1202	0.9659577	0.5985721	21
method	Eagle - SHAPEIT	0	0.0005987	1.75e-05	1202	34.2731192	0.0000000	21
method	Beagle - Eagle	0	-0.0007039	2.04e-05	1202	-34.4670939	0.0000000	22
method	Beagle - SHAPEIT	0	0.0001287	2.04e-05	1202	6.3018574	0.0000000	22
method	Eagle - SHAPEIT	0	0.0008326	2.04e-05	1202	40.7689512	0.0000000	22
method	Beagle - Eagle	0	-0.0005897	8.00e-06	1998	-73.8229089	0.0000000	23
method	Beagle - SHAPEIT	0	0.0001345	8.00e-06	1998	16.8434174	0.0000000	23
method	Eagle - SHAPEIT	0	0.0007242	8.00e-06	1998	90.6663262	0.0000000	23

Now let’s do these comparisons within each super-population:

mod_fit <- df_switches %>%
  filter(chrom == 1) %>%
  pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  {lmerTest::lmer(error_rate ~ method*SUPER + (1|pair_id), data = .)}

df_pop_anova <- anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = 1)

df_pop_pairwise <- emmeans::emmeans(mod_fit, ~ method | SUPER) %>% pairs() %>% broom::tidy() %>% mutate(chrom=1)
df_pop_pop <- emmeans::emmeans(mod_fit, ~ SUPER | method) %>% pairs() %>% broom::tidy() %>% mutate(chrom = 1)

for(i in 2:23){
  mod_fit <- df_switches %>%
    filter(chrom == i) %>%
    pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
    {lmerTest::lmer(error_rate ~ method*SUPER + (1|pair_id), data = .)}
  
  df_pop_anova <- df_pop_anova %>% bind_rows({anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = i)})
  df_pop_pairwise <- df_pop_pairwise %>% bind_rows({
    emmeans::emmeans(mod_fit, ~ method | SUPER) %>% pairs() %>% broom::tidy() %>% mutate(chrom=i)})
  df_pop_pop <- df_pop_pop %>% bind_rows({
    emmeans::emmeans(mod_fit, ~ SUPER | method) %>% pairs() %>% broom::tidy() %>% mutate(chrom = i)})
}

df_pop_anova %>% 
  knitr::kable()

term	sumsq	meansq	NumDF	DenDF	statistic	p.value	chrom
method	0.0001496	0.0000748	2	1194.0000	5014.194390	0e+00	1
SUPER	0.0000119	0.0000030	4	597.0000	198.717719	0e+00	1
method:SUPER	0.0000065	0.0000008	8	1194.0000	54.685913	0e+00	1
method	0.0001496	0.0000748	2	1194.0000	5442.934800	0e+00	2
SUPER	0.0000107	0.0000027	4	597.0000	195.359641	0e+00	2
method:SUPER	0.0000053	0.0000007	8	1194.0000	48.193179	0e+00	2
method	0.0001310	0.0000655	2	1194.0000	4748.229364	0e+00	3
SUPER	0.0000103	0.0000026	4	597.0000	186.224720	0e+00	3
method:SUPER	0.0000054	0.0000007	8	1194.0000	48.543572	0e+00	3
method	0.0001206	0.0000603	2	1194.0000	4736.804165	0e+00	4
SUPER	0.0000093	0.0000023	4	597.0000	182.688205	0e+00	4
method:SUPER	0.0000050	0.0000006	8	1194.0000	49.047522	0e+00	4
method	0.0001233	0.0000616	2	1194.0000	3954.352609	0e+00	5
SUPER	0.0000112	0.0000028	4	597.0000	179.972326	0e+00	5
method:SUPER	0.0000055	0.0000007	8	1194.0000	43.907671	0e+00	5
method	0.0001032	0.0000516	2	1194.0000	3663.509419	0e+00	6
SUPER	0.0000088	0.0000022	4	597.0000	156.487220	0e+00	6
method:SUPER	0.0000051	0.0000006	8	1194.0000	45.144347	0e+00	6
method	0.0001337	0.0000668	2	1194.0000	3768.753240	0e+00	7
SUPER	0.0000115	0.0000029	4	597.0000	161.880271	0e+00	7
method:SUPER	0.0000041	0.0000005	8	1194.0000	28.879945	0e+00	7
method	0.0001302	0.0000651	2	1194.0000	3415.028099	0e+00	8
SUPER	0.0000135	0.0000034	4	597.0000	177.569924	0e+00	8
method:SUPER	0.0000050	0.0000006	8	1194.0000	33.019615	0e+00	8
method	0.0001626	0.0000813	2	1194.0000	2648.080634	0e+00	9
SUPER	0.0000224	0.0000056	4	597.0000	182.298694	0e+00	9
method:SUPER	0.0000088	0.0000011	8	1194.0000	35.873591	0e+00	9
method	0.0001466	0.0000733	2	1194.0001	3844.572265	0e+00	10
SUPER	0.0000143	0.0000036	4	596.9998	187.814753	0e+00	10
method:SUPER	0.0000053	0.0000007	8	1194.0001	34.614194	0e+00	10
method	0.0001444	0.0000722	2	1194.0000	3424.093674	0e+00	11
SUPER	0.0000146	0.0000036	4	597.0000	172.872772	0e+00	11
method:SUPER	0.0000057	0.0000007	8	1194.0000	34.027636	0e+00	11
method	0.0001250	0.0000625	2	1194.0000	1281.508285	0e+00	12
SUPER	0.0000196	0.0000049	4	597.0000	100.644592	0e+00	12
method:SUPER	0.0000049	0.0000006	8	1194.0000	12.632958	0e+00	12
method	0.0001392	0.0000696	2	1194.0000	2498.343364	0e+00	13
SUPER	0.0000207	0.0000052	4	597.0000	185.557054	0e+00	13
method:SUPER	0.0000081	0.0000010	8	1194.0000	36.167211	0e+00	13
method	0.0001579	0.0000790	2	1194.0000	2382.681969	0e+00	14
SUPER	0.0000190	0.0000047	4	597.0000	142.990364	0e+00	14
method:SUPER	0.0000071	0.0000009	8	1194.0000	26.699004	0e+00	14
method	0.0001845	0.0000923	2	1194.0000	1932.907282	0e+00	15
SUPER	0.0000278	0.0000069	4	597.0000	145.522159	0e+00	15
method:SUPER	0.0000071	0.0000009	8	1194.0000	18.509090	0e+00	15
method	0.0002177	0.0001088	2	1194.0000	2078.946898	0e+00	16
SUPER	0.0000297	0.0000074	4	597.0000	141.765615	0e+00	16
method:SUPER	0.0000060	0.0000007	8	1194.0000	14.308354	0e+00	16
method	0.0002308	0.0001154	2	1194.0000	2230.086249	0e+00	17
SUPER	0.0000338	0.0000084	4	597.0000	163.231753	0e+00	17
method:SUPER	0.0000067	0.0000008	8	1194.0000	16.297216	0e+00	17
method	0.0001554	0.0000777	2	1194.0000	2002.049963	0e+00	18
SUPER	0.0000280	0.0000070	4	597.0000	180.156650	0e+00	18
method:SUPER	0.0000061	0.0000008	8	1194.0000	19.764112	0e+00	18
method	0.0001904	0.0000952	2	1194.0000	1705.412390	0e+00	19
SUPER	0.0000361	0.0000090	4	597.0000	161.480118	0e+00	19
method:SUPER	0.0000030	0.0000004	8	1194.0000	6.764480	0e+00	19
method	0.0001931	0.0000965	2	1194.0000	1723.663367	0e+00	20
SUPER	0.0000365	0.0000091	4	597.0000	162.938879	0e+00	20
method:SUPER	0.0000037	0.0000005	8	1194.0000	8.156113	0e+00	20
method	0.0001375	0.0000687	2	1194.0000	779.869376	0e+00	21
SUPER	0.0000295	0.0000074	4	597.0000	83.703338	0e+00	21
method:SUPER	0.0000052	0.0000006	8	1194.0000	7.321987	0e+00	21
method	0.0002223	0.0001111	2	1194.0000	915.286997	0e+00	22
SUPER	0.0000468	0.0000117	4	597.0000	96.401595	0e+00	22
method:SUPER	0.0000059	0.0000007	8	1194.0000	6.071499	1e-07	22
method	0.0002968	0.0001484	2	1990.0001	6292.933267	0e+00	23
SUPER	0.0000360	0.0000090	4	994.9997	382.040973	0e+00	23
method:SUPER	0.0000168	0.0000021	8	1990.0001	89.146795	0e+00	23

df_pop_pairwise %>% knitr::kable()

SUPER	term	contrast	null.value	estimate	std.error	df	statistic	adj.p.value	chrom
AFR	method	Beagle - Eagle	0	-0.0004848	1.22e-05	1194	-39.7886413	0.0000000	1
AFR	method	Beagle - SHAPEIT	0	0.0000661	1.22e-05	1194	5.4284702	0.0000002	1
AFR	method	Eagle - SHAPEIT	0	0.0005509	1.22e-05	1194	45.2171115	0.0000000	1
AMR	method	Beagle - Eagle	0	-0.0005501	1.48e-05	1194	-37.2747818	0.0000000	1
AMR	method	Beagle - SHAPEIT	0	0.0000178	1.48e-05	1194	1.2073952	0.4489875	1
AMR	method	Eagle - SHAPEIT	0	0.0005679	1.48e-05	1194	38.4821771	0.0000000	1
EAS	method	Beagle - Eagle	0	-0.0009117	2.04e-05	1194	-44.7834375	0.0000000	1
EAS	method	Beagle - SHAPEIT	0	-0.0000324	2.04e-05	1194	-1.5938996	0.2486367	1
EAS	method	Eagle - SHAPEIT	0	0.0008792	2.04e-05	1194	43.1895380	0.0000000	1
EUR	method	Beagle - Eagle	0	-0.0005309	1.67e-05	1194	-31.7907575	0.0000000	1
EUR	method	Beagle - SHAPEIT	0	0.0000564	1.67e-05	1194	3.3777776	0.0021759	1
EUR	method	Eagle - SHAPEIT	0	0.0005873	1.67e-05	1194	35.1685350	0.0000000	1
SAS	method	Beagle - Eagle	0	-0.0007155	1.87e-05	1194	-38.1900539	0.0000000	1
SAS	method	Beagle - SHAPEIT	0	0.0000169	1.87e-05	1194	0.9045021	0.6375561	1
SAS	method	Eagle - SHAPEIT	0	0.0007325	1.87e-05	1194	39.0945559	0.0000000	1
AFR	method	Beagle - Eagle	0	-0.0005135	1.17e-05	1194	-43.9081743	0.0000000	2
AFR	method	Beagle - SHAPEIT	0	0.0000462	1.17e-05	1194	3.9533922	0.0002405	2
AFR	method	Eagle - SHAPEIT	0	0.0005597	1.17e-05	1194	47.8615665	0.0000000	2
AMR	method	Beagle - Eagle	0	-0.0005781	1.42e-05	1194	-40.8112466	0.0000000	2
AMR	method	Beagle - SHAPEIT	0	0.0000021	1.42e-05	1194	0.1459337	0.9883278	2
AMR	method	Eagle - SHAPEIT	0	0.0005802	1.42e-05	1194	40.9571804	0.0000000	2
EAS	method	Beagle - Eagle	0	-0.0008646	1.95e-05	1194	-44.2511853	0.0000000	2
EAS	method	Beagle - SHAPEIT	0	-0.0000195	1.95e-05	1194	-0.9962264	0.5793828	2
EAS	method	Eagle - SHAPEIT	0	0.0008452	1.95e-05	1194	43.2549589	0.0000000	2
EUR	method	Beagle - Eagle	0	-0.0005174	1.60e-05	1194	-32.2778534	0.0000000	2
EUR	method	Beagle - SHAPEIT	0	0.0000417	1.60e-05	1194	2.5993975	0.0255885	2
EUR	method	Eagle - SHAPEIT	0	0.0005590	1.60e-05	1194	34.8772509	0.0000000	2
SAS	method	Beagle - Eagle	0	-0.0007434	1.80e-05	1194	-41.3411389	0.0000000	2
SAS	method	Beagle - SHAPEIT	0	0.0000085	1.80e-05	1194	0.4730133	0.8840124	2
SAS	method	Eagle - SHAPEIT	0	0.0007520	1.80e-05	1194	41.8141522	0.0000000	2
AFR	method	Beagle - Eagle	0	-0.0004931	1.17e-05	1194	-42.0962550	0.0000000	3
AFR	method	Beagle - SHAPEIT	0	0.0000332	1.17e-05	1194	2.8309661	0.0130887	3
AFR	method	Eagle - SHAPEIT	0	0.0005263	1.17e-05	1194	44.9272211	0.0000000	3
AMR	method	Beagle - Eagle	0	-0.0005221	1.42e-05	1194	-36.7974736	0.0000000	3
AMR	method	Beagle - SHAPEIT	0	-0.0000014	1.42e-05	1194	-0.0967627	0.9948513	3
AMR	method	Eagle - SHAPEIT	0	0.0005208	1.42e-05	1194	36.7007109	0.0000000	3
EAS	method	Beagle - Eagle	0	-0.0008802	1.96e-05	1194	-44.9693004	0.0000000	3
EAS	method	Beagle - SHAPEIT	0	-0.0000600	1.96e-05	1194	-3.0639246	0.0063175	3
EAS	method	Eagle - SHAPEIT	0	0.0008202	1.96e-05	1194	41.9053758	0.0000000	3
EUR	method	Beagle - Eagle	0	-0.0005040	1.61e-05	1194	-31.3906136	0.0000000	3
EUR	method	Beagle - SHAPEIT	0	0.0000200	1.61e-05	1194	1.2430270	0.4280413	3
EUR	method	Eagle - SHAPEIT	0	0.0005240	1.61e-05	1194	32.6336406	0.0000000	3
SAS	method	Beagle - Eagle	0	-0.0006650	1.80e-05	1194	-36.9150451	0.0000000	3
SAS	method	Beagle - SHAPEIT	0	-0.0000259	1.80e-05	1194	-1.4402671	0.3205575	3
SAS	method	Eagle - SHAPEIT	0	0.0006390	1.80e-05	1194	35.4747780	0.0000000	3
AFR	method	Beagle - Eagle	0	-0.0004339	1.13e-05	1194	-38.5466075	0.0000000	4
AFR	method	Beagle - SHAPEIT	0	0.0000511	1.13e-05	1194	4.5354027	0.0000189	4
AFR	method	Eagle - SHAPEIT	0	0.0004850	1.13e-05	1194	43.0820103	0.0000000	4
AMR	method	Beagle - Eagle	0	-0.0005228	1.36e-05	1194	-38.3434378	0.0000000	4
AMR	method	Beagle - SHAPEIT	0	-0.0000083	1.36e-05	1194	-0.6119203	0.8136340	4
AMR	method	Eagle - SHAPEIT	0	0.0005145	1.36e-05	1194	37.7315175	0.0000000	4
EAS	method	Beagle - Eagle	0	-0.0008400	1.88e-05	1194	-44.6613885	0.0000000	4
EAS	method	Beagle - SHAPEIT	0	-0.0000973	1.88e-05	1194	-5.1753282	0.0000008	4
EAS	method	Eagle - SHAPEIT	0	0.0007427	1.88e-05	1194	39.4860602	0.0000000	4
EUR	method	Beagle - Eagle	0	-0.0005122	1.54e-05	1194	-33.1984219	0.0000000	4
EUR	method	Beagle - SHAPEIT	0	0.0000316	1.54e-05	1194	2.0483651	0.1013175	4
EUR	method	Eagle - SHAPEIT	0	0.0005438	1.54e-05	1194	35.2467870	0.0000000	4
SAS	method	Beagle - Eagle	0	-0.0006292	1.73e-05	1194	-36.3475660	0.0000000	4
SAS	method	Beagle - SHAPEIT	0	-0.0000036	1.73e-05	1194	-0.2056646	0.9769522	4
SAS	method	Eagle - SHAPEIT	0	0.0006256	1.73e-05	1194	36.1419015	0.0000000	4
AFR	method	Beagle - Eagle	0	-0.0004639	1.25e-05	1194	-37.2522381	0.0000000	5
AFR	method	Beagle - SHAPEIT	0	0.0000540	1.25e-05	1194	4.3384791	0.0000462	5
AFR	method	Eagle - SHAPEIT	0	0.0005179	1.25e-05	1194	41.5907172	0.0000000	5
AMR	method	Beagle - Eagle	0	-0.0005029	1.51e-05	1194	-33.3397329	0.0000000	5
AMR	method	Beagle - SHAPEIT	0	-0.0000430	1.51e-05	1194	-2.8510091	0.0123197	5
AMR	method	Eagle - SHAPEIT	0	0.0004599	1.51e-05	1194	30.4887238	0.0000000	5
EAS	method	Beagle - Eagle	0	-0.0008289	2.08e-05	1194	-39.8393654	0.0000000	5
EAS	method	Beagle - SHAPEIT	0	-0.0000365	2.08e-05	1194	-1.7549461	0.1854418	5
EAS	method	Eagle - SHAPEIT	0	0.0007924	2.08e-05	1194	38.0844193	0.0000000	5
EUR	method	Beagle - Eagle	0	-0.0004968	1.71e-05	1194	-29.1088093	0.0000000	5
EUR	method	Beagle - SHAPEIT	0	0.0000271	1.71e-05	1194	1.5904161	0.2501429	5
EUR	method	Eagle - SHAPEIT	0	0.0005240	1.71e-05	1194	30.6992255	0.0000000	5
SAS	method	Beagle - Eagle	0	-0.0006651	1.91e-05	1194	-34.7312289	0.0000000	5
SAS	method	Beagle - SHAPEIT	0	-0.0000041	1.91e-05	1194	-0.2146232	0.9749268	5
SAS	method	Eagle - SHAPEIT	0	0.0006610	1.91e-05	1194	34.5166057	0.0000000	5
AFR	method	Beagle - Eagle	0	-0.0004307	1.18e-05	1194	-36.3778360	0.0000000	6
AFR	method	Beagle - SHAPEIT	0	0.0000395	1.18e-05	1194	3.3358343	0.0025230	6
AFR	method	Eagle - SHAPEIT	0	0.0004702	1.18e-05	1194	39.7136703	0.0000000	6
AMR	method	Beagle - Eagle	0	-0.0004455	1.43e-05	1194	-31.0634768	0.0000000	6
AMR	method	Beagle - SHAPEIT	0	-0.0000004	1.43e-05	1194	-0.0313327	0.9994589	6
AMR	method	Eagle - SHAPEIT	0	0.0004450	1.43e-05	1194	31.0321440	0.0000000	6
EAS	method	Beagle - Eagle	0	-0.0007786	1.98e-05	1194	-39.3551654	0.0000000	6
EAS	method	Beagle - SHAPEIT	0	-0.0000307	1.98e-05	1194	-1.5516019	0.2673213	6
EAS	method	Eagle - SHAPEIT	0	0.0007479	1.98e-05	1194	37.8035635	0.0000000	6
EUR	method	Beagle - Eagle	0	-0.0004135	1.62e-05	1194	-25.4785216	0.0000000	6
EUR	method	Beagle - SHAPEIT	0	0.0000458	1.62e-05	1194	2.8216635	0.0134599	6
EUR	method	Eagle - SHAPEIT	0	0.0004593	1.62e-05	1194	28.3001851	0.0000000	6
SAS	method	Beagle - Eagle	0	-0.0006084	1.82e-05	1194	-33.4147698	0.0000000	6
SAS	method	Beagle - SHAPEIT	0	0.0000028	1.82e-05	1194	0.1563964	0.9866059	6
SAS	method	Eagle - SHAPEIT	0	0.0006112	1.82e-05	1194	33.5711662	0.0000000	6
AFR	method	Beagle - Eagle	0	-0.0004893	1.33e-05	1194	-36.8384796	0.0000000	7
AFR	method	Beagle - SHAPEIT	0	0.0000892	1.33e-05	1194	6.7173393	0.0000000	7
AFR	method	Eagle - SHAPEIT	0	0.0005786	1.33e-05	1194	43.5558189	0.0000000	7
AMR	method	Beagle - Eagle	0	-0.0005097	1.61e-05	1194	-31.6815991	0.0000000	7
AMR	method	Beagle - SHAPEIT	0	0.0000040	1.61e-05	1194	0.2492418	0.9663358	7
AMR	method	Eagle - SHAPEIT	0	0.0005138	1.61e-05	1194	31.9308409	0.0000000	7
EAS	method	Beagle - Eagle	0	-0.0007787	2.22e-05	1194	-35.0853954	0.0000000	7
EAS	method	Beagle - SHAPEIT	0	-0.0000207	2.22e-05	1194	-0.9311449	0.6206665	7
EAS	method	Eagle - SHAPEIT	0	0.0007580	2.22e-05	1194	34.1542505	0.0000000	7
EUR	method	Beagle - Eagle	0	-0.0005095	1.82e-05	1194	-27.9878866	0.0000000	7
EUR	method	Beagle - SHAPEIT	0	0.0000678	1.82e-05	1194	3.7233301	0.0006025	7
EUR	method	Eagle - SHAPEIT	0	0.0005773	1.82e-05	1194	31.7112167	0.0000000	7
SAS	method	Beagle - Eagle	0	-0.0007076	2.04e-05	1194	-34.6411363	0.0000000	7
SAS	method	Beagle - SHAPEIT	0	0.0000208	2.04e-05	1194	1.0166939	0.5664368	7
SAS	method	Eagle - SHAPEIT	0	0.0007284	2.04e-05	1194	35.6578302	0.0000000	7
AFR	method	Beagle - Eagle	0	-0.0004810	1.38e-05	1194	-34.9313325	0.0000000	8
AFR	method	Beagle - SHAPEIT	0	0.0000378	1.38e-05	1194	2.7462505	0.0168314	8
AFR	method	Eagle - SHAPEIT	0	0.0005188	1.38e-05	1194	37.6775830	0.0000000	8
AMR	method	Beagle - Eagle	0	-0.0005401	1.67e-05	1194	-32.3807908	0.0000000	8
AMR	method	Beagle - SHAPEIT	0	-0.0000497	1.67e-05	1194	-2.9810694	0.0082364	8
AMR	method	Eagle - SHAPEIT	0	0.0004904	1.67e-05	1194	29.3997213	0.0000000	8
EAS	method	Beagle - Eagle	0	-0.0008343	2.30e-05	1194	-36.2603564	0.0000000	8
EAS	method	Beagle - SHAPEIT	0	-0.0000144	2.30e-05	1194	-0.6280035	0.8047548	8
EAS	method	Eagle - SHAPEIT	0	0.0008198	2.30e-05	1194	35.6323529	0.0000000	8
EUR	method	Beagle - Eagle	0	-0.0005210	1.89e-05	1194	-27.6024083	0.0000000	8
EUR	method	Beagle - SHAPEIT	0	0.0000243	1.89e-05	1194	1.2881028	0.4021488	8
EUR	method	Eagle - SHAPEIT	0	0.0005453	1.89e-05	1194	28.8905111	0.0000000	8
SAS	method	Beagle - Eagle	0	-0.0006606	2.12e-05	1194	-31.1944125	0.0000000	8
SAS	method	Beagle - SHAPEIT	0	0.0000044	2.12e-05	1194	0.2061953	0.9768345	8
SAS	method	Eagle - SHAPEIT	0	0.0006649	2.12e-05	1194	31.4006078	0.0000000	8
AFR	method	Beagle - Eagle	0	-0.0005045	1.75e-05	1194	-28.8649690	0.0000000	9
AFR	method	Beagle - SHAPEIT	0	0.0001140	1.75e-05	1194	6.5198154	0.0000000	9
AFR	method	Eagle - SHAPEIT	0	0.0006184	1.75e-05	1194	35.3847844	0.0000000	9
AMR	method	Beagle - Eagle	0	-0.0005468	2.12e-05	1194	-25.8310397	0.0000000	9
AMR	method	Beagle - SHAPEIT	0	0.0000109	2.12e-05	1194	0.5147044	0.8641932	9
AMR	method	Eagle - SHAPEIT	0	0.0005577	2.12e-05	1194	26.3457440	0.0000000	9
EAS	method	Beagle - Eagle	0	-0.0009980	2.92e-05	1194	-34.1746912	0.0000000	9
EAS	method	Beagle - SHAPEIT	0	-0.0000074	2.92e-05	1194	-0.2519426	0.9656152	9
EAS	method	Eagle - SHAPEIT	0	0.0009906	2.92e-05	1194	33.9227487	0.0000000	9
EUR	method	Beagle - Eagle	0	-0.0005329	2.40e-05	1194	-22.2458905	0.0000000	9
EUR	method	Beagle - SHAPEIT	0	0.0000734	2.40e-05	1194	3.0634042	0.0063281	9
EUR	method	Eagle - SHAPEIT	0	0.0006063	2.40e-05	1194	25.3092947	0.0000000	9
SAS	method	Beagle - Eagle	0	-0.0006835	2.69e-05	1194	-25.4290604	0.0000000	9
SAS	method	Beagle - SHAPEIT	0	0.0000554	2.69e-05	1194	2.0616579	0.0983708	9
SAS	method	Eagle - SHAPEIT	0	0.0007389	2.69e-05	1194	27.4907183	0.0000000	9
AFR	method	Beagle - Eagle	0	-0.0004960	1.38e-05	1194	-36.0113241	0.0000000	10
AFR	method	Beagle - SHAPEIT	0	0.0000833	1.38e-05	1194	6.0491303	0.0000000	10
AFR	method	Eagle - SHAPEIT	0	0.0005794	1.38e-05	1194	42.0604544	0.0000000	10
AMR	method	Beagle - Eagle	0	-0.0005394	1.67e-05	1194	-32.3266164	0.0000000	10
AMR	method	Beagle - SHAPEIT	0	0.0000218	1.67e-05	1194	1.3065352	0.3917706	10
AMR	method	Eagle - SHAPEIT	0	0.0005612	1.67e-05	1194	33.6331516	0.0000000	10
EAS	method	Beagle - Eagle	0	-0.0008549	2.30e-05	1194	-37.1449908	0.0000000	10
EAS	method	Beagle - SHAPEIT	0	-0.0000366	2.30e-05	1194	-1.5921365	0.2493983	10
EAS	method	Eagle - SHAPEIT	0	0.0008183	2.30e-05	1194	35.5528544	0.0000000	10
EUR	method	Beagle - Eagle	0	-0.0005128	1.89e-05	1194	-27.1635173	0.0000000	10
EUR	method	Beagle - SHAPEIT	0	0.0000779	1.89e-05	1194	4.1255422	0.0001171	10
EUR	method	Eagle - SHAPEIT	0	0.0005907	1.89e-05	1194	31.2890596	0.0000000	10
SAS	method	Beagle - Eagle	0	-0.0007367	2.12e-05	1194	-34.7767915	0.0000000	10
SAS	method	Beagle - SHAPEIT	0	0.0000168	2.12e-05	1194	0.7945323	0.7064651	10
SAS	method	Eagle - SHAPEIT	0	0.0007535	2.12e-05	1194	35.5713237	0.0000000	10
AFR	method	Beagle - Eagle	0	-0.0004786	1.45e-05	1194	-33.0405727	0.0000000	11
AFR	method	Beagle - SHAPEIT	0	0.0000427	1.45e-05	1194	2.9501043	0.0090788	11
AFR	method	Eagle - SHAPEIT	0	0.0005213	1.45e-05	1194	35.9906770	0.0000000	11
AMR	method	Beagle - Eagle	0	-0.0005509	1.75e-05	1194	-31.4030766	0.0000000	11
AMR	method	Beagle - SHAPEIT	0	-0.0000083	1.75e-05	1194	-0.4738340	0.8836342	11
AMR	method	Eagle - SHAPEIT	0	0.0005426	1.75e-05	1194	30.9292426	0.0000000	11
EAS	method	Beagle - Eagle	0	-0.0008302	2.42e-05	1194	-34.3054548	0.0000000	11
EAS	method	Beagle - SHAPEIT	0	-0.0000109	2.42e-05	1194	-0.4506925	0.8941073	11
EAS	method	Eagle - SHAPEIT	0	0.0008193	2.42e-05	1194	33.8547623	0.0000000	11
EUR	method	Beagle - Eagle	0	-0.0005410	1.99e-05	1194	-27.2504504	0.0000000	11
EUR	method	Beagle - SHAPEIT	0	0.0000536	1.99e-05	1194	2.6978328	0.0193706	11
EUR	method	Eagle - SHAPEIT	0	0.0005945	1.99e-05	1194	29.9482832	0.0000000	11
SAS	method	Beagle - Eagle	0	-0.0007511	2.23e-05	1194	-33.7229615	0.0000000	11
SAS	method	Beagle - SHAPEIT	0	0.0000168	2.23e-05	1194	0.7552775	0.7304877	11
SAS	method	Eagle - SHAPEIT	0	0.0007679	2.23e-05	1194	34.4782391	0.0000000	11
AFR	method	Beagle - Eagle	0	-0.0004589	2.20e-05	1194	-20.8256958	0.0000000	12
AFR	method	Beagle - SHAPEIT	0	0.0000635	2.20e-05	1194	2.8832788	0.0111659	12
AFR	method	Eagle - SHAPEIT	0	0.0005224	2.20e-05	1194	23.7089746	0.0000000	12
AMR	method	Beagle - Eagle	0	-0.0005511	2.67e-05	1194	-20.6483653	0.0000000	12
AMR	method	Beagle - SHAPEIT	0	-0.0000322	2.67e-05	1194	-1.2069318	0.4492626	12
AMR	method	Eagle - SHAPEIT	0	0.0005188	2.67e-05	1194	19.4414335	0.0000000	12
EAS	method	Beagle - Eagle	0	-0.0008548	3.68e-05	1194	-23.2202870	0.0000000	12
EAS	method	Beagle - SHAPEIT	0	-0.0000677	3.68e-05	1194	-1.8391891	0.1573432	12
EAS	method	Eagle - SHAPEIT	0	0.0007871	3.68e-05	1194	21.3810979	0.0000000	12
EUR	method	Beagle - Eagle	0	-0.0005199	3.02e-05	1194	-17.2168144	0.0000000	12
EUR	method	Beagle - SHAPEIT	0	0.0000481	3.02e-05	1194	1.5921232	0.2494040	12
EUR	method	Eagle - SHAPEIT	0	0.0005680	3.02e-05	1194	18.8089376	0.0000000	12
SAS	method	Beagle - Eagle	0	-0.0006166	3.39e-05	1194	-18.1996848	0.0000000	12
SAS	method	Beagle - SHAPEIT	0	-0.0000593	3.39e-05	1194	-1.7505059	0.1870160	12
SAS	method	Eagle - SHAPEIT	0	0.0005573	3.39e-05	1194	16.4491788	0.0000000	12
AFR	method	Beagle - Eagle	0	-0.0004233	1.67e-05	1194	-25.4238689	0.0000000	13
AFR	method	Beagle - SHAPEIT	0	0.0000487	1.67e-05	1194	2.9265783	0.0097698	13
AFR	method	Eagle - SHAPEIT	0	0.0004720	1.67e-05	1194	28.3504472	0.0000000	13
AMR	method	Beagle - Eagle	0	-0.0005647	2.02e-05	1194	-28.0014711	0.0000000	13
AMR	method	Beagle - SHAPEIT	0	-0.0000380	2.02e-05	1194	-1.8847916	0.1435052	13
AMR	method	Eagle - SHAPEIT	0	0.0005267	2.02e-05	1194	26.1166794	0.0000000	13
EAS	method	Beagle - Eagle	0	-0.0008419	2.78e-05	1194	-30.2609517	0.0000000	13
EAS	method	Beagle - SHAPEIT	0	0.0000113	2.78e-05	1194	0.4072950	0.9126339	13
EAS	method	Eagle - SHAPEIT	0	0.0008532	2.78e-05	1194	30.6682467	0.0000000	13
EUR	method	Beagle - Eagle	0	-0.0005333	2.28e-05	1194	-23.3693402	0.0000000	13
EUR	method	Beagle - SHAPEIT	0	0.0000316	2.28e-05	1194	1.3833907	0.3499278	13
EUR	method	Eagle - SHAPEIT	0	0.0005649	2.28e-05	1194	24.7527310	0.0000000	13
SAS	method	Beagle - Eagle	0	-0.0007708	2.56e-05	1194	-30.1039942	0.0000000	13
SAS	method	Beagle - SHAPEIT	0	-0.0000377	2.56e-05	1194	-1.4730930	0.3042626	13
SAS	method	Eagle - SHAPEIT	0	0.0007331	2.56e-05	1194	28.6309012	0.0000000	13
AFR	method	Beagle - Eagle	0	-0.0004913	1.82e-05	1194	-27.0560426	0.0000000	14
AFR	method	Beagle - SHAPEIT	0	0.0000489	1.82e-05	1194	2.6920504	0.0196953	14
AFR	method	Eagle - SHAPEIT	0	0.0005402	1.82e-05	1194	29.7480930	0.0000000	14
AMR	method	Beagle - Eagle	0	-0.0006419	2.20e-05	1194	-29.1847896	0.0000000	14
AMR	method	Beagle - SHAPEIT	0	-0.0000436	2.20e-05	1194	-1.9799300	0.1176013	14
AMR	method	Eagle - SHAPEIT	0	0.0005984	2.20e-05	1194	27.2048596	0.0000000	14
EAS	method	Beagle - Eagle	0	-0.0009522	3.03e-05	1194	-31.3846202	0.0000000	14
EAS	method	Beagle - SHAPEIT	0	-0.0000641	3.03e-05	1194	-2.1128677	0.0876476	14
EAS	method	Eagle - SHAPEIT	0	0.0008881	3.03e-05	1194	29.2717525	0.0000000	14
EUR	method	Beagle - Eagle	0	-0.0005525	2.49e-05	1194	-22.1987473	0.0000000	14
EUR	method	Beagle - SHAPEIT	0	0.0000416	2.49e-05	1194	1.6694587	0.2174190	14
EUR	method	Eagle - SHAPEIT	0	0.0005941	2.49e-05	1194	23.8682061	0.0000000	14
SAS	method	Beagle - Eagle	0	-0.0007275	2.79e-05	1194	-26.0506668	0.0000000	14
SAS	method	Beagle - SHAPEIT	0	-0.0000211	2.79e-05	1194	-0.7555807	0.7303038	14
SAS	method	Eagle - SHAPEIT	0	0.0007064	2.79e-05	1194	25.2950861	0.0000000	14
AFR	method	Beagle - Eagle	0	-0.0005743	2.18e-05	1194	-26.3535930	0.0000000	15
AFR	method	Beagle - SHAPEIT	0	0.0001027	2.18e-05	1194	4.7125204	0.0000082	15
AFR	method	Eagle - SHAPEIT	0	0.0006770	2.18e-05	1194	31.0661134	0.0000000	15
AMR	method	Beagle - Eagle	0	-0.0006306	2.64e-05	1194	-23.8908757	0.0000000	15
AMR	method	Beagle - SHAPEIT	0	-0.0000201	2.64e-05	1194	-0.7612565	0.7268558	15
AMR	method	Eagle - SHAPEIT	0	0.0006105	2.64e-05	1194	23.1296193	0.0000000	15
EAS	method	Beagle - Eagle	0	-0.0009537	3.64e-05	1194	-26.1926143	0.0000000	15
EAS	method	Beagle - SHAPEIT	0	-0.0000241	3.64e-05	1194	-0.6622936	0.7854026	15
EAS	method	Eagle - SHAPEIT	0	0.0009296	3.64e-05	1194	25.5303207	0.0000000	15
EUR	method	Beagle - Eagle	0	-0.0005542	2.99e-05	1194	-18.5541847	0.0000000	15
EUR	method	Beagle - SHAPEIT	0	0.0000871	2.99e-05	1194	2.9145756	0.0101402	15
EUR	method	Eagle - SHAPEIT	0	0.0006412	2.99e-05	1194	21.4687603	0.0000000	15
SAS	method	Beagle - Eagle	0	-0.0008598	3.35e-05	1194	-25.6579923	0.0000000	15
SAS	method	Beagle - SHAPEIT	0	-0.0000582	3.35e-05	1194	-1.7365068	0.1920409	15
SAS	method	Eagle - SHAPEIT	0	0.0008016	3.35e-05	1194	23.9214854	0.0000000	15
AFR	method	Beagle - Eagle	0	-0.0006647	2.28e-05	1194	-29.1210527	0.0000000	16
AFR	method	Beagle - SHAPEIT	0	0.0001090	2.28e-05	1194	4.7765912	0.0000060	16
AFR	method	Eagle - SHAPEIT	0	0.0007737	2.28e-05	1194	33.8976439	0.0000000	16
AMR	method	Beagle - Eagle	0	-0.0006997	2.76e-05	1194	-25.3092022	0.0000000	16
AMR	method	Beagle - SHAPEIT	0	-0.0000309	2.76e-05	1194	-1.1176813	0.5033142	16
AMR	method	Eagle - SHAPEIT	0	0.0006688	2.76e-05	1194	24.1915209	0.0000000	16
EAS	method	Beagle - Eagle	0	-0.0010784	3.81e-05	1194	-28.2773994	0.0000000	16
EAS	method	Beagle - SHAPEIT	0	-0.0000907	3.81e-05	1194	-2.3774503	0.0462395	16
EAS	method	Eagle - SHAPEIT	0	0.0009877	3.81e-05	1194	25.8999491	0.0000000	16
EUR	method	Beagle - Eagle	0	-0.0007772	3.13e-05	1194	-24.8432150	0.0000000	16
EUR	method	Beagle - SHAPEIT	0	-0.0000458	3.13e-05	1194	-1.4641268	0.3086647	16
EUR	method	Eagle - SHAPEIT	0	0.0007314	3.13e-05	1194	23.3790882	0.0000000	16
SAS	method	Beagle - Eagle	0	-0.0007396	3.51e-05	1194	-21.0718950	0.0000000	16
SAS	method	Beagle - SHAPEIT	0	-0.0000035	3.51e-05	1194	-0.1006958	0.9944255	16
SAS	method	Eagle - SHAPEIT	0	0.0007361	3.51e-05	1194	20.9711992	0.0000000	16
AFR	method	Beagle - Eagle	0	-0.0006415	2.27e-05	1194	-28.2696810	0.0000000	17
AFR	method	Beagle - SHAPEIT	0	0.0000717	2.27e-05	1194	3.1609305	0.0045913	17
AFR	method	Eagle - SHAPEIT	0	0.0007132	2.27e-05	1194	31.4306115	0.0000000	17
AMR	method	Beagle - Eagle	0	-0.0006918	2.75e-05	1194	-25.1708871	0.0000000	17
AMR	method	Beagle - SHAPEIT	0	0.0000367	2.75e-05	1194	1.3359853	0.3754574	17
AMR	method	Eagle - SHAPEIT	0	0.0007285	2.75e-05	1194	26.5068724	0.0000000	17
EAS	method	Beagle - Eagle	0	-0.0009805	3.79e-05	1194	-25.8636477	0.0000000	17
EAS	method	Beagle - SHAPEIT	0	-0.0000490	3.79e-05	1194	-1.2933483	0.3991825	17
EAS	method	Eagle - SHAPEIT	0	0.0009315	3.79e-05	1194	24.5702994	0.0000000	17
EUR	method	Beagle - Eagle	0	-0.0006699	3.11e-05	1194	-21.5413492	0.0000000	17
EUR	method	Beagle - SHAPEIT	0	0.0000758	3.11e-05	1194	2.4366683	0.0396808	17
EUR	method	Eagle - SHAPEIT	0	0.0007457	3.11e-05	1194	23.9780175	0.0000000	17
SAS	method	Beagle - Eagle	0	-0.0009283	3.49e-05	1194	-26.6049770	0.0000000	17
SAS	method	Beagle - SHAPEIT	0	0.0001195	3.49e-05	1194	3.4239965	0.0018447	17
SAS	method	Eagle - SHAPEIT	0	0.0010478	3.49e-05	1194	30.0289735	0.0000000	17
AFR	method	Beagle - Eagle	0	-0.0005025	1.97e-05	1194	-25.5658666	0.0000000	18
AFR	method	Beagle - SHAPEIT	0	0.0000428	1.97e-05	1194	2.1777036	0.0754366	18
AFR	method	Eagle - SHAPEIT	0	0.0005453	1.97e-05	1194	27.7435702	0.0000000	18
AMR	method	Beagle - Eagle	0	-0.0005614	2.38e-05	1194	-23.5813399	0.0000000	18
AMR	method	Beagle - SHAPEIT	0	0.0000000	2.38e-05	1194	0.0002905	1.0000000	18
AMR	method	Eagle - SHAPEIT	0	0.0005614	2.38e-05	1194	23.5816303	0.0000000	18
EAS	method	Beagle - Eagle	0	-0.0009121	3.28e-05	1194	-27.7759201	0.0000000	18
EAS	method	Beagle - SHAPEIT	0	-0.0000483	3.28e-05	1194	-1.4697483	0.3059004	18
EAS	method	Eagle - SHAPEIT	0	0.0008638	3.28e-05	1194	26.3061718	0.0000000	18
EUR	method	Beagle - Eagle	0	-0.0005976	2.69e-05	1194	-22.1846501	0.0000000	18
EUR	method	Beagle - SHAPEIT	0	0.0000092	2.69e-05	1194	0.3427056	0.9373182	18
EUR	method	Eagle - SHAPEIT	0	0.0006068	2.69e-05	1194	22.5273557	0.0000000	18
SAS	method	Beagle - Eagle	0	-0.0007351	3.02e-05	1194	-24.3222096	0.0000000	18
SAS	method	Beagle - SHAPEIT	0	0.0000188	3.02e-05	1194	0.6236429	0.8071752	18
SAS	method	Eagle - SHAPEIT	0	0.0007539	3.02e-05	1194	24.9458524	0.0000000	18
AFR	method	Beagle - Eagle	0	-0.0006283	2.36e-05	1194	-26.6582969	0.0000000	19
AFR	method	Beagle - SHAPEIT	0	0.0001134	2.36e-05	1194	4.8108655	0.0000051	19
AFR	method	Eagle - SHAPEIT	0	0.0007417	2.36e-05	1194	31.4691625	0.0000000	19
AMR	method	Beagle - Eagle	0	-0.0006456	2.85e-05	1194	-22.6150649	0.0000000	19
AMR	method	Beagle - SHAPEIT	0	0.0000739	2.85e-05	1194	2.5897748	0.0262807	19
AMR	method	Eagle - SHAPEIT	0	0.0007196	2.85e-05	1194	25.2048397	0.0000000	19
EAS	method	Beagle - Eagle	0	-0.0009197	3.94e-05	1194	-23.3544515	0.0000000	19
EAS	method	Beagle - SHAPEIT	0	-0.0000075	3.94e-05	1194	-0.1904170	0.9802099	19
EAS	method	Eagle - SHAPEIT	0	0.0009122	3.94e-05	1194	23.1640345	0.0000000	19
EUR	method	Beagle - Eagle	0	-0.0006161	3.23e-05	1194	-19.0712235	0.0000000	19
EUR	method	Beagle - SHAPEIT	0	0.0000805	3.23e-05	1194	2.4910241	0.0343744	19
EUR	method	Eagle - SHAPEIT	0	0.0006965	3.23e-05	1194	21.5622476	0.0000000	19
SAS	method	Beagle - Eagle	0	-0.0007272	3.62e-05	1194	-20.0648596	0.0000000	19
SAS	method	Beagle - SHAPEIT	0	0.0000011	3.62e-05	1194	0.0311845	0.9994640	19
SAS	method	Eagle - SHAPEIT	0	0.0007284	3.62e-05	1194	20.0960441	0.0000000	19
AFR	method	Beagle - Eagle	0	-0.0005896	2.36e-05	1194	-24.9757304	0.0000000	20
AFR	method	Beagle - SHAPEIT	0	0.0001246	2.36e-05	1194	5.2772216	0.0000005	20
AFR	method	Eagle - SHAPEIT	0	0.0007142	2.36e-05	1194	30.2529520	0.0000000	20
AMR	method	Beagle - Eagle	0	-0.0006870	2.86e-05	1194	-24.0269211	0.0000000	20
AMR	method	Beagle - SHAPEIT	0	0.0000420	2.86e-05	1194	1.4674466	0.3070305	20
AMR	method	Eagle - SHAPEIT	0	0.0007290	2.86e-05	1194	25.4943677	0.0000000	20
EAS	method	Beagle - Eagle	0	-0.0008894	3.94e-05	1194	-22.5494096	0.0000000	20
EAS	method	Beagle - SHAPEIT	0	0.0000280	3.94e-05	1194	0.7087858	0.7583438	20
EAS	method	Eagle - SHAPEIT	0	0.0009174	3.94e-05	1194	23.2581954	0.0000000	20
EUR	method	Beagle - Eagle	0	-0.0005743	3.24e-05	1194	-17.7501488	0.0000000	20
EUR	method	Beagle - SHAPEIT	0	0.0001009	3.24e-05	1194	3.1198495	0.0052617	20
EUR	method	Eagle - SHAPEIT	0	0.0006753	3.24e-05	1194	20.8699983	0.0000000	20
SAS	method	Beagle - Eagle	0	-0.0007694	3.63e-05	1194	-21.1936667	0.0000000	20
SAS	method	Beagle - SHAPEIT	0	0.0000598	3.63e-05	1194	1.6469038	0.2264468	20
SAS	method	Eagle - SHAPEIT	0	0.0008292	3.63e-05	1194	22.8405705	0.0000000	20
AFR	method	Beagle - Eagle	0	-0.0004929	2.96e-05	1194	-16.6421645	0.0000000	21
AFR	method	Beagle - SHAPEIT	0	0.0000780	2.96e-05	1194	2.6323872	0.0233345	21
AFR	method	Eagle - SHAPEIT	0	0.0005708	2.96e-05	1194	19.2745517	0.0000000	21
AMR	method	Beagle - Eagle	0	-0.0005291	3.59e-05	1194	-14.7486978	0.0000000	21
AMR	method	Beagle - SHAPEIT	0	-0.0000607	3.59e-05	1194	-1.6918263	0.2087106	21
AMR	method	Eagle - SHAPEIT	0	0.0004684	3.59e-05	1194	13.0568715	0.0000000	21
EAS	method	Beagle - Eagle	0	-0.0008174	4.95e-05	1194	-16.5191428	0.0000000	21
EAS	method	Beagle - SHAPEIT	0	0.0000127	4.95e-05	1194	0.2563844	0.9644143	21
EAS	method	Eagle - SHAPEIT	0	0.0008301	4.95e-05	1194	16.7755272	0.0000000	21
EUR	method	Beagle - Eagle	0	-0.0005720	4.06e-05	1194	-14.0914190	0.0000000	21
EUR	method	Beagle - SHAPEIT	0	0.0000421	4.06e-05	1194	1.0366747	0.5538347	21
EUR	method	Eagle - SHAPEIT	0	0.0006140	4.06e-05	1194	15.1280937	0.0000000	21
SAS	method	Beagle - Eagle	0	-0.0006902	4.55e-05	1194	-15.1552930	0.0000000	21
SAS	method	Beagle - SHAPEIT	0	-0.0000307	4.55e-05	1194	-0.6750046	0.7780931	21
SAS	method	Eagle - SHAPEIT	0	0.0006594	4.55e-05	1194	14.4802884	0.0000000	21
AFR	method	Beagle - Eagle	0	-0.0006710	3.48e-05	1194	-19.3021432	0.0000000	22
AFR	method	Beagle - SHAPEIT	0	0.0002068	3.48e-05	1194	5.9504723	0.0000000	22
AFR	method	Eagle - SHAPEIT	0	0.0008778	3.48e-05	1194	25.2526155	0.0000000	22
AMR	method	Beagle - Eagle	0	-0.0006841	4.21e-05	1194	-16.2486012	0.0000000	22
AMR	method	Beagle - SHAPEIT	0	0.0000762	4.21e-05	1194	1.8101418	0.1666555	22
AMR	method	Eagle - SHAPEIT	0	0.0007604	4.21e-05	1194	18.0587430	0.0000000	22
EAS	method	Beagle - Eagle	0	-0.0009450	5.81e-05	1194	-16.2705031	0.0000000	22
EAS	method	Beagle - SHAPEIT	0	0.0001413	5.81e-05	1194	2.4335804	0.0400021	22
EAS	method	Eagle - SHAPEIT	0	0.0010863	5.81e-05	1194	18.7040835	0.0000000	22
EUR	method	Beagle - Eagle	0	-0.0005896	4.76e-05	1194	-12.3746919	0.0000000	22
EUR	method	Beagle - SHAPEIT	0	0.0000589	4.76e-05	1194	1.2353450	0.4325231	22
EUR	method	Eagle - SHAPEIT	0	0.0006484	4.76e-05	1194	13.6100369	0.0000000	22
SAS	method	Beagle - Eagle	0	-0.0007533	5.35e-05	1194	-14.0921321	0.0000000	22
SAS	method	Beagle - SHAPEIT	0	0.0001057	5.35e-05	1194	1.9773718	0.1182471	22
SAS	method	Eagle - SHAPEIT	0	0.0008590	5.35e-05	1194	16.0695039	0.0000000	22
AFR	method	Beagle - Eagle	0	-0.0004678	1.54e-05	1990	-30.4654146	0.0000000	23
AFR	method	Beagle - SHAPEIT	0	0.0001173	1.54e-05	1990	7.6403140	0.0000000	23
AFR	method	Eagle - SHAPEIT	0	0.0005851	1.54e-05	1990	38.1057286	0.0000000	23
AMR	method	Beagle - Eagle	0	-0.0004554	1.54e-05	1990	-29.6551906	0.0000000	23
AMR	method	Beagle - SHAPEIT	0	0.0000767	1.54e-05	1990	4.9958668	0.0000019	23
AMR	method	Eagle - SHAPEIT	0	0.0005321	1.54e-05	1990	34.6510575	0.0000000	23
EAS	method	Beagle - Eagle	0	-0.0008262	1.54e-05	1990	-53.8035422	0.0000000	23
EAS	method	Beagle - SHAPEIT	0	0.0001816	1.54e-05	1990	11.8266653	0.0000000	23
EAS	method	Eagle - SHAPEIT	0	0.0010078	1.54e-05	1990	65.6302076	0.0000000	23
EUR	method	Beagle - Eagle	0	-0.0005527	1.54e-05	1990	-35.9949554	0.0000000	23
EUR	method	Beagle - SHAPEIT	0	0.0001158	1.54e-05	1990	7.5391191	0.0000000	23
EUR	method	Eagle - SHAPEIT	0	0.0006685	1.54e-05	1990	43.5340745	0.0000000	23
SAS	method	Beagle - Eagle	0	-0.0006463	1.54e-05	1990	-42.0871894	0.0000000	23
SAS	method	Beagle - SHAPEIT	0	0.0001813	1.54e-05	1990	11.8061447	0.0000000	23
SAS	method	Eagle - SHAPEIT	0	0.0008275	1.54e-05	1990	53.8933341	0.0000000	23

df_pop_pop %>% knitr::kable()

method	term	contrast	null.value	estimate	std.error	df	statistic	adj.p.value	chrom
Beagle	SUPER	AFR - AMR	0	-0.0004807	0.0000669	630.7053	-7.1848755	0.0000000	1
Beagle	SUPER	AFR - EAS	0	-0.0018942	0.0000829	630.7053	-22.8393004	0.0000000	1
Beagle	SUPER	AFR - EUR	0	-0.0004813	0.0000723	630.7053	-6.6613280	0.0000000	1
Beagle	SUPER	AFR - SAS	0	-0.0013017	0.0000781	630.7053	-16.6613976	0.0000000	1
Beagle	SUPER	AMR - EAS	0	-0.0014135	0.0000879	630.7053	-16.0817395	0.0000000	1
Beagle	SUPER	AMR - EUR	0	-0.0000007	0.0000779	630.7053	-0.0089136	1.0000000	1
Beagle	SUPER	AMR - SAS	0	-0.0008210	0.0000834	630.7053	-9.8476033	0.0000000	1
Beagle	SUPER	EAS - EUR	0	0.0014128	0.0000920	630.7053	15.3496278	0.0000000	1
Beagle	SUPER	EAS - SAS	0	0.0005925	0.0000967	630.7053	6.1260957	0.0000000	1
Beagle	SUPER	EUR - SAS	0	-0.0008203	0.0000877	630.7053	-9.3501925	0.0000000	1
Eagle	SUPER	AFR - AMR	0	-0.0005460	0.0000669	630.7053	-8.1612259	0.0000000	1
Eagle	SUPER	AFR - EAS	0	-0.0023210	0.0000829	630.7053	-27.9865987	0.0000000	1
Eagle	SUPER	AFR - EUR	0	-0.0005274	0.0000723	630.7053	-7.2992369	0.0000000	1
Eagle	SUPER	AFR - SAS	0	-0.0015324	0.0000781	630.7053	-19.6149324	0.0000000	1
Eagle	SUPER	AMR - EAS	0	-0.0017751	0.0000879	630.7053	-20.1954142	0.0000000	1
Eagle	SUPER	AMR - EUR	0	0.0000185	0.0000779	630.7053	0.2378093	0.9992921	1
Eagle	SUPER	AMR - SAS	0	-0.0009864	0.0000834	630.7053	-11.8318237	0.0000000	1
Eagle	SUPER	EAS - EUR	0	0.0017936	0.0000920	630.7053	19.4867853	0.0000000	1
Eagle	SUPER	EAS - SAS	0	0.0007886	0.0000967	630.7053	8.1541414	0.0000000	1
Eagle	SUPER	EUR - SAS	0	-0.0010050	0.0000877	630.7053	-11.4548630	0.0000000	1
SHAPEIT	SUPER	AFR - AMR	0	-0.0005290	0.0000669	630.7053	-7.9071873	0.0000000	1
SHAPEIT	SUPER	AFR - EAS	0	-0.0019927	0.0000829	630.7053	-24.0280479	0.0000000	1
SHAPEIT	SUPER	AFR - EUR	0	-0.0004911	0.0000723	630.7053	-6.7960378	0.0000000	1
SHAPEIT	SUPER	AFR - SAS	0	-0.0013509	0.0000781	630.7053	-17.2910718	0.0000000	1
SHAPEIT	SUPER	AMR - EAS	0	-0.0014638	0.0000879	630.7053	-16.6536301	0.0000000	1
SHAPEIT	SUPER	AMR - EUR	0	0.0000379	0.0000779	630.7053	0.4864065	0.9886045	1
SHAPEIT	SUPER	AMR - SAS	0	-0.0008219	0.0000834	630.7053	-9.8580616	0.0000000	1
SHAPEIT	SUPER	EAS - EUR	0	0.0015017	0.0000920	630.7053	16.3149894	0.0000000	1
SHAPEIT	SUPER	EAS - SAS	0	0.0006419	0.0000967	630.7053	6.6368193	0.0000000	1
SHAPEIT	SUPER	EUR - SAS	0	-0.0008598	0.0000877	630.7053	-9.7999554	0.0000000	1
Beagle	SUPER	AFR - AMR	0	-0.0005297	0.0000643	630.6478	-8.2429775	0.0000000	2
Beagle	SUPER	AFR - EAS	0	-0.0018225	0.0000797	630.6478	-22.8765490	0.0000000	2
Beagle	SUPER	AFR - EUR	0	-0.0003888	0.0000694	630.6478	-5.6016983	0.0000003	2
Beagle	SUPER	AFR - SAS	0	-0.0012416	0.0000750	630.6478	-16.5441496	0.0000000	2
Beagle	SUPER	AMR - EAS	0	-0.0012928	0.0000844	630.6478	-15.3115428	0.0000000	2
Beagle	SUPER	AMR - EUR	0	0.0001409	0.0000748	630.6478	1.8825834	0.3277699	2
Beagle	SUPER	AMR - SAS	0	-0.0007119	0.0000801	630.6478	-8.8887089	0.0000000	2
Beagle	SUPER	EAS - EUR	0	0.0014337	0.0000884	630.6478	16.2150908	0.0000000	2
Beagle	SUPER	EAS - SAS	0	0.0005809	0.0000929	630.6478	6.2527494	0.0000000	2
Beagle	SUPER	EUR - SAS	0	-0.0008528	0.0000843	630.6478	-10.1185359	0.0000000	2
Eagle	SUPER	AFR - AMR	0	-0.0005943	0.0000643	630.6478	-9.2483756	0.0000000	2
Eagle	SUPER	AFR - EAS	0	-0.0021737	0.0000797	630.6478	-27.2843550	0.0000000	2
Eagle	SUPER	AFR - EUR	0	-0.0003927	0.0000694	630.6478	-5.6575273	0.0000002	2
Eagle	SUPER	AFR - SAS	0	-0.0014716	0.0000750	630.6478	-19.6083904	0.0000000	2
Eagle	SUPER	AMR - EAS	0	-0.0015793	0.0000844	630.6478	-18.7053518	0.0000000	2
Eagle	SUPER	AMR - EUR	0	0.0002016	0.0000748	630.6478	2.6941653	0.0559223	2
Eagle	SUPER	AMR - SAS	0	-0.0008772	0.0000801	630.6478	-10.9533597	0.0000000	2
Eagle	SUPER	EAS - EUR	0	0.0017810	0.0000884	630.6478	20.1429117	0.0000000	2
Eagle	SUPER	EAS - SAS	0	0.0007021	0.0000929	630.6478	7.5572399	0.0000000	2
Eagle	SUPER	EUR - SAS	0	-0.0010789	0.0000843	630.6478	-12.8012112	0.0000000	2
SHAPEIT	SUPER	AFR - AMR	0	-0.0005739	0.0000643	630.6478	-8.9302327	0.0000000	2
SHAPEIT	SUPER	AFR - EAS	0	-0.0018882	0.0000797	630.6478	-23.7012034	0.0000000	2
SHAPEIT	SUPER	AFR - EUR	0	-0.0003934	0.0000694	630.6478	-5.6675196	0.0000002	2
SHAPEIT	SUPER	AFR - SAS	0	-0.0012793	0.0000750	630.6478	-17.0468442	0.0000000	2
SHAPEIT	SUPER	AMR - EAS	0	-0.0013143	0.0000844	630.6478	-15.5665712	0.0000000	2
SHAPEIT	SUPER	AMR - EUR	0	0.0001805	0.0000748	630.6478	2.4116975	0.1134719	2
SHAPEIT	SUPER	AMR - SAS	0	-0.0007054	0.0000801	630.6478	-8.8083088	0.0000000	2
SHAPEIT	SUPER	EAS - EUR	0	0.0014948	0.0000884	630.6478	16.9064698	0.0000000	2
SHAPEIT	SUPER	EAS - SAS	0	0.0006089	0.0000929	630.6478	6.5538305	0.0000000	2
SHAPEIT	SUPER	EUR - SAS	0	-0.0008859	0.0000843	630.6478	-10.5119645	0.0000000	2
Beagle	SUPER	AFR - AMR	0	-0.0004770	0.0000612	634.3251	-7.7901000	0.0000000	3
Beagle	SUPER	AFR - EAS	0	-0.0016633	0.0000759	634.3251	-21.9124039	0.0000000	3
Beagle	SUPER	AFR - EUR	0	-0.0004289	0.0000661	634.3251	-6.4854370	0.0000000	3
Beagle	SUPER	AFR - SAS	0	-0.0011775	0.0000715	634.3251	-16.4669982	0.0000000	3
Beagle	SUPER	AMR - EAS	0	-0.0011863	0.0000804	634.3251	-14.7465064	0.0000000	3
Beagle	SUPER	AMR - EUR	0	0.0000481	0.0000713	634.3251	0.6739613	0.9619775	3
Beagle	SUPER	AMR - SAS	0	-0.0007005	0.0000763	634.3251	-9.1798041	0.0000000	3
Beagle	SUPER	EAS - EUR	0	0.0012344	0.0000842	634.3251	14.6525376	0.0000000	3
Beagle	SUPER	EAS - SAS	0	0.0004858	0.0000885	634.3251	5.4883007	0.0000006	3
Beagle	SUPER	EUR - SAS	0	-0.0007486	0.0000803	634.3251	-9.3219533	0.0000000	3
Eagle	SUPER	AFR - AMR	0	-0.0005060	0.0000612	634.3251	-8.2636234	0.0000000	3
Eagle	SUPER	AFR - EAS	0	-0.0020504	0.0000759	634.3251	-27.0112230	0.0000000	3
Eagle	SUPER	AFR - EUR	0	-0.0004398	0.0000661	634.3251	-6.6496732	0.0000000	3
Eagle	SUPER	AFR - SAS	0	-0.0013493	0.0000715	634.3251	-18.8703182	0.0000000	3
Eagle	SUPER	AMR - EAS	0	-0.0015444	0.0000804	634.3251	-19.1971499	0.0000000	3
Eagle	SUPER	AMR - EUR	0	0.0000662	0.0000713	634.3251	0.9282515	0.8859266	3
Eagle	SUPER	AMR - SAS	0	-0.0008434	0.0000763	634.3251	-11.0519090	0.0000000	3
Eagle	SUPER	EAS - EUR	0	0.0016106	0.0000842	634.3251	19.1178867	0.0000000	3
Eagle	SUPER	EAS - SAS	0	0.0007010	0.0000885	634.3251	7.9192358	0.0000000	3
Eagle	SUPER	EUR - SAS	0	-0.0009095	0.0000803	634.3251	-11.3268008	0.0000000	3
SHAPEIT	SUPER	AFR - AMR	0	-0.0005115	0.0000612	634.3251	-8.3541310	0.0000000	3
SHAPEIT	SUPER	AFR - EAS	0	-0.0017565	0.0000759	634.3251	-23.1393189	0.0000000	3
SHAPEIT	SUPER	AFR - EUR	0	-0.0004421	0.0000661	634.3251	-6.6851015	0.0000000	3
SHAPEIT	SUPER	AFR - SAS	0	-0.0012366	0.0000715	634.3251	-17.2936082	0.0000000	3
SHAPEIT	SUPER	AMR - EAS	0	-0.0012449	0.0000804	634.3251	-15.4748812	0.0000000	3
SHAPEIT	SUPER	AMR - EUR	0	0.0000694	0.0000713	634.3251	0.9731112	0.8672733	3
SHAPEIT	SUPER	AMR - SAS	0	-0.0007251	0.0000763	634.3251	-9.5018087	0.0000000	3
SHAPEIT	SUPER	EAS - EUR	0	0.0013143	0.0000842	634.3251	15.6012950	0.0000000	3
SHAPEIT	SUPER	EAS - SAS	0	0.0005199	0.0000885	634.3251	5.8726699	0.0000001	3
SHAPEIT	SUPER	EUR - SAS	0	-0.0007945	0.0000803	634.3251	-9.8935853	0.0000000	3
Beagle	SUPER	AFR - AMR	0	-0.0005064	0.0000560	638.4437	-9.0510630	0.0000000	4
Beagle	SUPER	AFR - EAS	0	-0.0014302	0.0000694	638.4437	-20.6181250	0.0000000	4
Beagle	SUPER	AFR - EUR	0	-0.0003830	0.0000604	638.4437	-6.3378211	0.0000000	4
Beagle	SUPER	AFR - SAS	0	-0.0011164	0.0000653	638.4437	-17.0851905	0.0000000	4
Beagle	SUPER	AMR - EAS	0	-0.0009237	0.0000735	638.4437	-12.5655292	0.0000000	4
Beagle	SUPER	AMR - EUR	0	0.0001234	0.0000652	638.4437	1.8937125	0.3217099	4
Beagle	SUPER	AMR - SAS	0	-0.0006100	0.0000697	638.4437	-8.7472869	0.0000000	4
Beagle	SUPER	EAS - EUR	0	0.0010471	0.0000770	638.4437	13.6022193	0.0000000	4
Beagle	SUPER	EAS - SAS	0	0.0003138	0.0000809	638.4437	3.8790612	0.0010923	4
Beagle	SUPER	EUR - SAS	0	-0.0007333	0.0000734	638.4437	-9.9940258	0.0000000	4
Eagle	SUPER	AFR - AMR	0	-0.0005953	0.0000560	638.4437	-10.6399188	0.0000000	4
Eagle	SUPER	AFR - EAS	0	-0.0018363	0.0000694	638.4437	-26.4726774	0.0000000	4
Eagle	SUPER	AFR - EUR	0	-0.0004613	0.0000604	638.4437	-7.6331995	0.0000000	4
Eagle	SUPER	AFR - SAS	0	-0.0013117	0.0000653	638.4437	-20.0737380	0.0000000	4
Eagle	SUPER	AMR - EAS	0	-0.0012409	0.0000735	638.4437	-16.8803516	0.0000000	4
Eagle	SUPER	AMR - EUR	0	0.0001340	0.0000652	638.4437	2.0565696	0.2405037	4
Eagle	SUPER	AMR - SAS	0	-0.0007163	0.0000697	638.4437	-10.2728393	0.0000000	4
Eagle	SUPER	EAS - EUR	0	0.0013749	0.0000770	638.4437	17.8604780	0.0000000	4
Eagle	SUPER	EAS - SAS	0	0.0005246	0.0000809	638.4437	6.4853065	0.0000000	4
Eagle	SUPER	EUR - SAS	0	-0.0008503	0.0000734	638.4437	-11.5883580	0.0000000	4
SHAPEIT	SUPER	AFR - AMR	0	-0.0005658	0.0000560	638.4437	-10.1126598	0.0000000	4
SHAPEIT	SUPER	AFR - EAS	0	-0.0015786	0.0000694	638.4437	-22.7574952	0.0000000	4
SHAPEIT	SUPER	AFR - EUR	0	-0.0004025	0.0000604	638.4437	-6.6596682	0.0000000	4
SHAPEIT	SUPER	AFR - SAS	0	-0.0011710	0.0000653	638.4437	-17.9210263	0.0000000	4
SHAPEIT	SUPER	AMR - EAS	0	-0.0010127	0.0000735	638.4437	-13.7761545	0.0000000	4
SHAPEIT	SUPER	AMR - EUR	0	0.0001633	0.0000652	638.4437	2.5068059	0.0903563	4
SHAPEIT	SUPER	AMR - SAS	0	-0.0006052	0.0000697	638.4437	-8.6786878	0.0000000	4
SHAPEIT	SUPER	EAS - EUR	0	0.0011761	0.0000770	638.4437	15.2772203	0.0000000	4
SHAPEIT	SUPER	EAS - SAS	0	0.0004076	0.0000809	638.4437	5.0384239	0.0000061	4
SHAPEIT	SUPER	EUR - SAS	0	-0.0007685	0.0000734	638.4437	-10.4732390	0.0000000	4
Beagle	SUPER	AFR - AMR	0	-0.0004595	0.0000644	635.1412	-7.1333934	0.0000000	5
Beagle	SUPER	AFR - EAS	0	-0.0017015	0.0000799	635.1412	-21.3077225	0.0000000	5
Beagle	SUPER	AFR - EUR	0	-0.0004053	0.0000696	635.1412	-5.8257167	0.0000001	5
Beagle	SUPER	AFR - SAS	0	-0.0012484	0.0000752	635.1412	-16.5953891	0.0000000	5
Beagle	SUPER	AMR - EAS	0	-0.0012420	0.0000846	635.1412	-14.6757849	0.0000000	5
Beagle	SUPER	AMR - EUR	0	0.0000542	0.0000750	635.1412	0.7219579	0.9514281	5
Beagle	SUPER	AMR - SAS	0	-0.0007889	0.0000803	635.1412	-9.8270587	0.0000000	5
Beagle	SUPER	EAS - EUR	0	0.0012962	0.0000886	635.1412	14.6256267	0.0000000	5
Beagle	SUPER	EAS - SAS	0	0.0004531	0.0000931	635.1412	4.8660624	0.0000142	5
Beagle	SUPER	EUR - SAS	0	-0.0008430	0.0000845	635.1412	-9.9796538	0.0000000	5
Eagle	SUPER	AFR - AMR	0	-0.0004985	0.0000644	635.1412	-7.7386505	0.0000000	5
Eagle	SUPER	AFR - EAS	0	-0.0020665	0.0000799	635.1412	-25.8787000	0.0000000	5
Eagle	SUPER	AFR - EUR	0	-0.0004383	0.0000696	635.1412	-6.2988992	0.0000000	5
Eagle	SUPER	AFR - SAS	0	-0.0014496	0.0000752	635.1412	-19.2698312	0.0000000	5
Eagle	SUPER	AMR - EAS	0	-0.0015681	0.0000846	635.1412	-18.5281119	0.0000000	5
Eagle	SUPER	AMR - EUR	0	0.0000602	0.0000750	635.1412	0.8028052	0.9297348	5
Eagle	SUPER	AMR - SAS	0	-0.0009511	0.0000803	635.1412	-11.8475185	0.0000000	5
Eagle	SUPER	EAS - EUR	0	0.0016283	0.0000886	635.1412	18.3728150	0.0000000	5
Eagle	SUPER	EAS - SAS	0	0.0006170	0.0000931	635.1412	6.6253528	0.0000000	5
Eagle	SUPER	EUR - SAS	0	-0.0010113	0.0000845	635.1412	-11.9714716	0.0000000	5
SHAPEIT	SUPER	AFR - AMR	0	-0.0005565	0.0000644	635.1412	-8.6396912	0.0000000	5
SHAPEIT	SUPER	AFR - EAS	0	-0.0017921	0.0000799	635.1412	-22.4415111	0.0000000	5
SHAPEIT	SUPER	AFR - EUR	0	-0.0004322	0.0000696	635.1412	-6.2120620	0.0000000	5
SHAPEIT	SUPER	AFR - SAS	0	-0.0013065	0.0000752	635.1412	-17.3682064	0.0000000	5
SHAPEIT	SUPER	AMR - EAS	0	-0.0012355	0.0000846	635.1412	-14.5991105	0.0000000	5
SHAPEIT	SUPER	AMR - EUR	0	0.0001243	0.0000750	635.1412	1.6571039	0.4614777	5
SHAPEIT	SUPER	AMR - SAS	0	-0.0007500	0.0000803	635.1412	-9.3425772	0.0000000	5
SHAPEIT	SUPER	EAS - EUR	0	0.0013598	0.0000886	635.1412	15.3439122	0.0000000	5
SHAPEIT	SUPER	EAS - SAS	0	0.0004855	0.0000931	635.1412	5.2140274	0.0000025	5
SHAPEIT	SUPER	EUR - SAS	0	-0.0008743	0.0000845	635.1412	-10.3496270	0.0000000	5
Beagle	SUPER	AFR - AMR	0	-0.0003974	0.0000584	639.1428	-6.8068381	0.0000000	6
Beagle	SUPER	AFR - EAS	0	-0.0014009	0.0000724	639.1428	-19.3561855	0.0000000	6
Beagle	SUPER	AFR - EUR	0	-0.0003120	0.0000631	639.1428	-4.9483428	0.0000095	6
Beagle	SUPER	AFR - SAS	0	-0.0010676	0.0000682	639.1428	-15.6596456	0.0000000	6
Beagle	SUPER	AMR - EAS	0	-0.0010035	0.0000767	639.1428	-13.0829367	0.0000000	6
Beagle	SUPER	AMR - EUR	0	0.0000853	0.0000680	639.1428	1.2553529	0.7186647	6
Beagle	SUPER	AMR - SAS	0	-0.0006703	0.0000728	639.1428	-9.2122375	0.0000000	6
Beagle	SUPER	EAS - EUR	0	0.0010888	0.0000803	639.1428	13.5560089	0.0000000	6
Beagle	SUPER	EAS - SAS	0	0.0003332	0.0000844	639.1428	3.9484748	0.0008292	6
Beagle	SUPER	EUR - SAS	0	-0.0007556	0.0000766	639.1428	-9.8690271	0.0000000	6
Eagle	SUPER	AFR - AMR	0	-0.0004122	0.0000584	639.1428	-7.0599745	0.0000000	6
Eagle	SUPER	AFR - EAS	0	-0.0017487	0.0000724	639.1428	-24.1622959	0.0000000	6
Eagle	SUPER	AFR - EUR	0	-0.0002948	0.0000631	639.1428	-4.6747109	0.0000353	6
Eagle	SUPER	AFR - SAS	0	-0.0012453	0.0000682	639.1428	-18.2656881	0.0000000	6
Eagle	SUPER	AMR - EAS	0	-0.0013366	0.0000767	639.1428	-17.4251325	0.0000000	6
Eagle	SUPER	AMR - EUR	0	0.0001174	0.0000680	639.1428	1.7265394	0.4183083	6
Eagle	SUPER	AMR - SAS	0	-0.0008331	0.0000728	639.1428	-11.4511457	0.0000000	6
Eagle	SUPER	EAS - EUR	0	0.0014539	0.0000803	639.1428	18.1013769	0.0000000	6
Eagle	SUPER	EAS - SAS	0	0.0005034	0.0000844	639.1428	5.9646487	0.0000000	6
Eagle	SUPER	EUR - SAS	0	-0.0009505	0.0000766	639.1428	-12.4150405	0.0000000	6
SHAPEIT	SUPER	AFR - AMR	0	-0.0004373	0.0000584	639.1428	-7.4910772	0.0000000	6
SHAPEIT	SUPER	AFR - EAS	0	-0.0014711	0.0000724	639.1428	-20.3260321	0.0000000	6
SHAPEIT	SUPER	AFR - EUR	0	-0.0003057	0.0000631	639.1428	-4.8485485	0.0000154	6
SHAPEIT	SUPER	AFR - SAS	0	-0.0011043	0.0000682	639.1428	-16.1971999	0.0000000	6
SHAPEIT	SUPER	AMR - EAS	0	-0.0010337	0.0000767	639.1428	-13.4772586	0.0000000	6
SHAPEIT	SUPER	AMR - EUR	0	0.0001316	0.0000680	639.1428	1.9354957	0.2995529	6
SHAPEIT	SUPER	AMR - SAS	0	-0.0006670	0.0000728	639.1428	-9.1669233	0.0000000	6
SHAPEIT	SUPER	EAS - EUR	0	0.0011653	0.0000803	639.1428	14.5082357	0.0000000	6
SHAPEIT	SUPER	EAS - SAS	0	0.0003668	0.0000844	639.1428	4.3459012	0.0001567	6
SHAPEIT	SUPER	EUR - SAS	0	-0.0007985	0.0000766	639.1428	-10.4299050	0.0000000	6
Beagle	SUPER	AFR - AMR	0	-0.0003883	0.0000653	639.4150	-5.9473862	0.0000000	7
Beagle	SUPER	AFR - EAS	0	-0.0016532	0.0000809	639.4150	-20.4228820	0.0000000	7
Beagle	SUPER	AFR - EUR	0	-0.0003161	0.0000705	639.4150	-4.4819484	0.0000856	7
Beagle	SUPER	AFR - SAS	0	-0.0011325	0.0000763	639.4150	-14.8523711	0.0000000	7
Beagle	SUPER	AMR - EAS	0	-0.0012648	0.0000858	639.4150	-14.7435774	0.0000000	7
Beagle	SUPER	AMR - EUR	0	0.0000722	0.0000760	639.4150	0.9499242	0.8771082	7
Beagle	SUPER	AMR - SAS	0	-0.0007442	0.0000814	639.4150	-9.1453984	0.0000000	7
Beagle	SUPER	EAS - EUR	0	0.0013370	0.0000898	639.4150	14.8833148	0.0000000	7
Beagle	SUPER	EAS - SAS	0	0.0005206	0.0000944	639.4150	5.5152983	0.0000005	7
Beagle	SUPER	EUR - SAS	0	-0.0008164	0.0000856	639.4150	-9.5343018	0.0000000	7
Eagle	SUPER	AFR - AMR	0	-0.0004087	0.0000653	639.4150	-6.2599081	0.0000000	7
Eagle	SUPER	AFR - EAS	0	-0.0019425	0.0000809	639.4150	-23.9975453	0.0000000	7
Eagle	SUPER	AFR - EUR	0	-0.0003363	0.0000705	639.4150	-4.7684742	0.0000227	7
Eagle	SUPER	AFR - SAS	0	-0.0013508	0.0000763	639.4150	-17.7147460	0.0000000	7
Eagle	SUPER	AMR - EAS	0	-0.0015338	0.0000858	639.4150	-17.8786270	0.0000000	7
Eagle	SUPER	AMR - EUR	0	0.0000724	0.0000760	639.4150	0.9525262	0.8760251	7
Eagle	SUPER	AMR - SAS	0	-0.0009421	0.0000814	639.4150	-11.5768551	0.0000000	7
Eagle	SUPER	EAS - EUR	0	0.0016062	0.0000898	639.4150	17.8793162	0.0000000	7
Eagle	SUPER	EAS - SAS	0	0.0005917	0.0000944	639.4150	6.2684207	0.0000000	7
Eagle	SUPER	EUR - SAS	0	-0.0010145	0.0000856	639.4150	-11.8472083	0.0000000	7
SHAPEIT	SUPER	AFR - AMR	0	-0.0004736	0.0000653	639.4150	-7.2525270	0.0000000	7
SHAPEIT	SUPER	AFR - EAS	0	-0.0017630	0.0000809	639.4150	-21.7805175	0.0000000	7
SHAPEIT	SUPER	AFR - EUR	0	-0.0003375	0.0000705	639.4150	-4.7859682	0.0000208	7
SHAPEIT	SUPER	AFR - SAS	0	-0.0012010	0.0000763	639.4150	-15.7501966	0.0000000	7
SHAPEIT	SUPER	AMR - EAS	0	-0.0012895	0.0000858	639.4150	-15.0312212	0.0000000	7
SHAPEIT	SUPER	AMR - EUR	0	0.0001360	0.0000760	639.4150	1.7886923	0.3810372	7
SHAPEIT	SUPER	AMR - SAS	0	-0.0007274	0.0000814	639.4150	-8.9394667	0.0000000	7
SHAPEIT	SUPER	EAS - EUR	0	0.0014255	0.0000898	639.4150	15.8679301	0.0000000	7
SHAPEIT	SUPER	EAS - SAS	0	0.0005621	0.0000944	639.4150	5.9542350	0.0000000	7
SHAPEIT	SUPER	EUR - SAS	0	-0.0008634	0.0000856	639.4150	-10.0833992	0.0000000	7
Beagle	SUPER	AFR - AMR	0	-0.0005456	0.0000651	643.0653	-8.3848693	0.0000000	8
Beagle	SUPER	AFR - EAS	0	-0.0017805	0.0000807	643.0653	-22.0729241	0.0000000	8
Beagle	SUPER	AFR - EUR	0	-0.0004309	0.0000703	643.0653	-6.1306601	0.0000000	8
Beagle	SUPER	AFR - SAS	0	-0.0011871	0.0000760	643.0653	-15.6221860	0.0000000	8
Beagle	SUPER	AMR - EAS	0	-0.0012349	0.0000855	643.0653	-14.4452760	0.0000000	8
Beagle	SUPER	AMR - EUR	0	0.0001147	0.0000758	643.0653	1.5137856	0.5538420	8
Beagle	SUPER	AMR - SAS	0	-0.0006415	0.0000811	643.0653	-7.9109164	0.0000000	8
Beagle	SUPER	EAS - EUR	0	0.0013496	0.0000895	643.0653	15.0757045	0.0000000	8
Beagle	SUPER	EAS - SAS	0	0.0005934	0.0000941	643.0653	6.3083850	0.0000000	8
Beagle	SUPER	EUR - SAS	0	-0.0007562	0.0000853	643.0653	-8.8618689	0.0000000	8
Eagle	SUPER	AFR - AMR	0	-0.0006047	0.0000651	643.0653	-9.2928435	0.0000000	8
Eagle	SUPER	AFR - EAS	0	-0.0021338	0.0000807	643.0653	-26.4523747	0.0000000	8
Eagle	SUPER	AFR - EUR	0	-0.0004708	0.0000703	643.0653	-6.6988873	0.0000000	8
Eagle	SUPER	AFR - SAS	0	-0.0013666	0.0000760	643.0653	-17.9850130	0.0000000	8
Eagle	SUPER	AMR - EAS	0	-0.0015291	0.0000855	643.0653	-17.8864814	0.0000000	8
Eagle	SUPER	AMR - EUR	0	0.0001338	0.0000758	643.0653	1.7664259	0.3942179	8
Eagle	SUPER	AMR - SAS	0	-0.0007620	0.0000811	643.0653	-9.3964716	0.0000000	8
Eagle	SUPER	EAS - EUR	0	0.0016630	0.0000895	643.0653	18.5756994	0.0000000	8
Eagle	SUPER	EAS - SAS	0	0.0007671	0.0000941	643.0653	8.1551592	0.0000000	8
Eagle	SUPER	EUR - SAS	0	-0.0008958	0.0000853	643.0653	-10.4979159	0.0000000	8
SHAPEIT	SUPER	AFR - AMR	0	-0.0006331	0.0000651	643.0653	-9.7302632	0.0000000	8
SHAPEIT	SUPER	AFR - EAS	0	-0.0018328	0.0000807	643.0653	-22.7208813	0.0000000	8
SHAPEIT	SUPER	AFR - EUR	0	-0.0004444	0.0000703	643.0653	-6.3228291	0.0000000	8
SHAPEIT	SUPER	AFR - SAS	0	-0.0012205	0.0000760	643.0653	-16.0624092	0.0000000	8
SHAPEIT	SUPER	AMR - EAS	0	-0.0011996	0.0000855	643.0653	-14.0326569	0.0000000	8
SHAPEIT	SUPER	AMR - EUR	0	0.0001887	0.0000758	643.0653	2.4908690	0.0939318	8
SHAPEIT	SUPER	AMR - SAS	0	-0.0005874	0.0000811	643.0653	-7.2438832	0.0000000	8
SHAPEIT	SUPER	EAS - EUR	0	0.0013884	0.0000895	643.0653	15.5086769	0.0000000	8
SHAPEIT	SUPER	EAS - SAS	0	0.0006122	0.0000941	643.0653	6.5084093	0.0000000	8
SHAPEIT	SUPER	EUR - SAS	0	-0.0007762	0.0000853	643.0653	-9.0956031	0.0000000	8
Beagle	SUPER	AFR - AMR	0	-0.0003911	0.0000759	652.0586	-5.1557551	0.0000033	9
Beagle	SUPER	AFR - EAS	0	-0.0020236	0.0000941	652.0586	-21.5162240	0.0000000	9
Beagle	SUPER	AFR - EUR	0	-0.0005123	0.0000819	652.0586	-6.2518878	0.0000000	9
Beagle	SUPER	AFR - SAS	0	-0.0013780	0.0000886	652.0586	-15.5537726	0.0000000	9
Beagle	SUPER	AMR - EAS	0	-0.0016325	0.0000997	652.0586	-16.3777400	0.0000000	9
Beagle	SUPER	AMR - EUR	0	-0.0001212	0.0000883	652.0586	-1.3716019	0.6461377	9
Beagle	SUPER	AMR - SAS	0	-0.0009869	0.0000945	652.0586	-10.4378640	0.0000000	9
Beagle	SUPER	EAS - EUR	0	0.0015113	0.0001044	652.0586	14.4789160	0.0000000	9
Beagle	SUPER	EAS - SAS	0	0.0006456	0.0001097	652.0586	5.8862691	0.0000001	9
Beagle	SUPER	EUR - SAS	0	-0.0008657	0.0000995	652.0586	-8.7011001	0.0000000	9
Eagle	SUPER	AFR - AMR	0	-0.0004335	0.0000759	652.0586	-5.7140026	0.0000002	9
Eagle	SUPER	AFR - EAS	0	-0.0025171	0.0000941	652.0586	-26.7632832	0.0000000	9
Eagle	SUPER	AFR - EUR	0	-0.0005407	0.0000819	652.0586	-6.5984590	0.0000000	9
Eagle	SUPER	AFR - SAS	0	-0.0015570	0.0000886	652.0586	-17.5736207	0.0000000	9
Eagle	SUPER	AMR - EAS	0	-0.0020836	0.0000997	652.0586	-20.9037721	0.0000000	9
Eagle	SUPER	AMR - EUR	0	-0.0001072	0.0000883	652.0586	-1.2136834	0.7434499	9
Eagle	SUPER	AMR - SAS	0	-0.0011235	0.0000945	652.0586	-11.8826488	0.0000000	9
Eagle	SUPER	EAS - EUR	0	0.0019764	0.0001044	652.0586	18.9346882	0.0000000	9
Eagle	SUPER	EAS - SAS	0	0.0009601	0.0001097	652.0586	8.7540894	0.0000000	9
Eagle	SUPER	EUR - SAS	0	-0.0010163	0.0000995	652.0586	-10.2142941	0.0000000	9
SHAPEIT	SUPER	AFR - AMR	0	-0.0004942	0.0000759	652.0586	-6.5141598	0.0000000	9
SHAPEIT	SUPER	AFR - EAS	0	-0.0021449	0.0000941	652.0586	-22.8060605	0.0000000	9
SHAPEIT	SUPER	AFR - EUR	0	-0.0005529	0.0000819	652.0586	-6.7469542	0.0000000	9
SHAPEIT	SUPER	AFR - SAS	0	-0.0014366	0.0000886	652.0586	-16.2145361	0.0000000	9
SHAPEIT	SUPER	AMR - EAS	0	-0.0016507	0.0000997	652.0586	-16.5608711	0.0000000	9
SHAPEIT	SUPER	AMR - EUR	0	-0.0000587	0.0000883	652.0586	-0.6643017	0.9639017	9
SHAPEIT	SUPER	AMR - SAS	0	-0.0009424	0.0000945	652.0586	-9.9670512	0.0000000	9
SHAPEIT	SUPER	EAS - EUR	0	0.0015920	0.0001044	652.0586	15.2524531	0.0000000	9
SHAPEIT	SUPER	EAS - SAS	0	0.0007084	0.0001097	652.0586	6.4585646	0.0000000	9
SHAPEIT	SUPER	EUR - SAS	0	-0.0008837	0.0000995	652.0586	-8.8817444	0.0000000	9
Beagle	SUPER	AFR - AMR	0	-0.0004560	0.0000632	646.0101	-7.2155670	0.0000000	10
Beagle	SUPER	AFR - EAS	0	-0.0016612	0.0000783	646.0101	-21.2058333	0.0000000	10
Beagle	SUPER	AFR - EUR	0	-0.0003958	0.0000683	646.0101	-5.7992752	0.0000001	10
Beagle	SUPER	AFR - SAS	0	-0.0012602	0.0000738	646.0101	-17.0771050	0.0000000	10
Beagle	SUPER	AMR - EAS	0	-0.0012053	0.0000830	646.0101	-14.5171021	0.0000000	10
Beagle	SUPER	AMR - EUR	0	0.0000601	0.0000736	646.0101	0.8170491	0.9253880	10
Beagle	SUPER	AMR - SAS	0	-0.0008043	0.0000788	646.0101	-10.2125204	0.0000000	10
Beagle	SUPER	EAS - EUR	0	0.0012654	0.0000869	646.0101	14.5545783	0.0000000	10
Beagle	SUPER	EAS - SAS	0	0.0004010	0.0000914	646.0101	4.3895627	0.0001291	10
Beagle	SUPER	EUR - SAS	0	-0.0008644	0.0000829	646.0101	-10.4303925	0.0000000	10
Eagle	SUPER	AFR - AMR	0	-0.0004993	0.0000632	646.0101	-7.9010580	0.0000000	10
Eagle	SUPER	AFR - EAS	0	-0.0020201	0.0000783	646.0101	-25.7866915	0.0000000	10
Eagle	SUPER	AFR - EUR	0	-0.0004126	0.0000683	646.0101	-6.0452018	0.0000000	10
Eagle	SUPER	AFR - SAS	0	-0.0015008	0.0000738	646.0101	-20.3375258	0.0000000	10
Eagle	SUPER	AMR - EAS	0	-0.0015208	0.0000830	646.0101	-18.3176845	0.0000000	10
Eagle	SUPER	AMR - EUR	0	0.0000867	0.0000736	646.0101	1.1775897	0.7642543	10
Eagle	SUPER	AMR - SAS	0	-0.0010015	0.0000788	646.0101	-12.7176990	0.0000000	10
Eagle	SUPER	EAS - EUR	0	0.0016075	0.0000869	646.0101	18.4890851	0.0000000	10
Eagle	SUPER	EAS - SAS	0	0.0005193	0.0000914	646.0101	5.6839751	0.0000002	10
Eagle	SUPER	EUR - SAS	0	-0.0010882	0.0000829	646.0101	-13.1311916	0.0000000	10
SHAPEIT	SUPER	AFR - AMR	0	-0.0005175	0.0000632	646.0101	-8.1892208	0.0000000	10
SHAPEIT	SUPER	AFR - EAS	0	-0.0017812	0.0000783	646.0101	-22.7372628	0.0000000	10
SHAPEIT	SUPER	AFR - EUR	0	-0.0004013	0.0000683	646.0101	-5.8789343	0.0000001	10
SHAPEIT	SUPER	AFR - SAS	0	-0.0013267	0.0000738	646.0101	-17.9781811	0.0000000	10
SHAPEIT	SUPER	AMR - EAS	0	-0.0012637	0.0000830	646.0101	-15.2210328	0.0000000	10
SHAPEIT	SUPER	AMR - EUR	0	0.0001162	0.0000736	646.0101	1.5792674	0.5112671	10
SHAPEIT	SUPER	AMR - SAS	0	-0.0008092	0.0000788	646.0101	-10.2756213	0.0000000	10
SHAPEIT	SUPER	EAS - EUR	0	0.0013799	0.0000869	646.0101	15.8719329	0.0000000	10
SHAPEIT	SUPER	EAS - SAS	0	0.0004545	0.0000914	646.0101	4.9749049	0.0000083	10
SHAPEIT	SUPER	EUR - SAS	0	-0.0009254	0.0000829	646.0101	-11.1671763	0.0000000	10
Beagle	SUPER	AFR - AMR	0	-0.0005333	0.0000673	644.6732	-7.9205795	0.0000000	11
Beagle	SUPER	AFR - EAS	0	-0.0017392	0.0000835	644.6732	-20.8383111	0.0000000	11
Beagle	SUPER	AFR - EUR	0	-0.0004278	0.0000727	644.6732	-5.8826704	0.0000001	11
Beagle	SUPER	AFR - SAS	0	-0.0012997	0.0000786	644.6732	-16.5309460	0.0000000	11
Beagle	SUPER	AMR - EAS	0	-0.0012060	0.0000885	644.6732	-13.6337227	0.0000000	11
Beagle	SUPER	AMR - EUR	0	0.0001055	0.0000784	644.6732	1.3451111	0.6630158	11
Beagle	SUPER	AMR - SAS	0	-0.0007665	0.0000839	644.6732	-9.1350299	0.0000000	11
Beagle	SUPER	EAS - EUR	0	0.0013114	0.0000926	644.6732	14.1579502	0.0000000	11
Beagle	SUPER	EAS - SAS	0	0.0004395	0.0000973	644.6732	4.5155908	0.0000734	11
Beagle	SUPER	EUR - SAS	0	-0.0008719	0.0000883	644.6732	-9.8753590	0.0000000	11
Eagle	SUPER	AFR - AMR	0	-0.0006056	0.0000673	644.6732	-8.9955370	0.0000000	11
Eagle	SUPER	AFR - EAS	0	-0.0020909	0.0000835	644.6732	-25.0513804	0.0000000	11
Eagle	SUPER	AFR - EUR	0	-0.0004902	0.0000727	644.6732	-6.7407832	0.0000000	11
Eagle	SUPER	AFR - SAS	0	-0.0015723	0.0000786	644.6732	-19.9973909	0.0000000	11
Eagle	SUPER	AMR - EAS	0	-0.0014852	0.0000885	644.6732	-16.7908425	0.0000000	11
Eagle	SUPER	AMR - EUR	0	0.0001154	0.0000784	644.6732	1.4722585	0.5809442	11
Eagle	SUPER	AMR - SAS	0	-0.0009666	0.0000839	644.6732	-11.5207565	0.0000000	11
Eagle	SUPER	EAS - EUR	0	0.0016007	0.0000926	644.6732	17.2804423	0.0000000	11
Eagle	SUPER	EAS - SAS	0	0.0005186	0.0000973	644.6732	5.3281924	0.0000014	11
Eagle	SUPER	EUR - SAS	0	-0.0010821	0.0000883	644.6732	-12.2553998	0.0000000	11
SHAPEIT	SUPER	AFR - AMR	0	-0.0005843	0.0000673	644.6732	-8.6787111	0.0000000	11
SHAPEIT	SUPER	AFR - EAS	0	-0.0017929	0.0000835	644.6732	-21.4809339	0.0000000	11
SHAPEIT	SUPER	AFR - EUR	0	-0.0004170	0.0000727	644.6732	-5.7337916	0.0000002	11
SHAPEIT	SUPER	AFR - SAS	0	-0.0013256	0.0000786	644.6732	-16.8604480	0.0000000	11
SHAPEIT	SUPER	AMR - EAS	0	-0.0012086	0.0000885	644.6732	-13.6630476	0.0000000	11
SHAPEIT	SUPER	AMR - EUR	0	0.0001673	0.0000784	644.6732	2.1342368	0.2068323	11
SHAPEIT	SUPER	AMR - SAS	0	-0.0007413	0.0000839	644.6732	-8.8354659	0.0000000	11
SHAPEIT	SUPER	EAS - EUR	0	0.0013759	0.0000926	644.6732	14.8538678	0.0000000	11
SHAPEIT	SUPER	EAS - SAS	0	0.0004672	0.0000973	644.6732	4.8004807	0.0000194	11
SHAPEIT	SUPER	EUR - SAS	0	-0.0009087	0.0000883	644.6732	-10.2913976	0.0000000	11
Beagle	SUPER	AFR - AMR	0	-0.0004762	0.0000951	652.7626	-5.0094721	0.0000070	12
Beagle	SUPER	AFR - EAS	0	-0.0017950	0.0001179	652.7626	-15.2314551	0.0000000	12
Beagle	SUPER	AFR - EUR	0	-0.0004501	0.0001027	652.7626	-4.3837139	0.0001322	12
Beagle	SUPER	AFR - SAS	0	-0.0014503	0.0001110	652.7626	-13.0638189	0.0000000	12
Beagle	SUPER	AMR - EAS	0	-0.0013188	0.0001249	652.7626	-10.5590101	0.0000000	12
Beagle	SUPER	AMR - EUR	0	0.0000261	0.0001107	652.7626	0.2356264	0.9993175	12
Beagle	SUPER	AMR - SAS	0	-0.0009741	0.0001185	652.7626	-8.2219988	0.0000000	12
Beagle	SUPER	EAS - EUR	0	0.0013449	0.0001308	652.7626	10.2827046	0.0000000	12
Beagle	SUPER	EAS - SAS	0	0.0003447	0.0001374	652.7626	2.5083439	0.0899880	12
Beagle	SUPER	EUR - SAS	0	-0.0010002	0.0001247	652.7626	-8.0225338	0.0000000	12
Eagle	SUPER	AFR - AMR	0	-0.0005684	0.0000951	652.7626	-5.9793994	0.0000000	12
Eagle	SUPER	AFR - EAS	0	-0.0021910	0.0001179	652.7626	-18.5913293	0.0000000	12
Eagle	SUPER	AFR - EUR	0	-0.0005112	0.0001027	652.7626	-4.9783823	0.0000081	12
Eagle	SUPER	AFR - SAS	0	-0.0016081	0.0001110	652.7626	-14.4850317	0.0000000	12
Eagle	SUPER	AMR - EAS	0	-0.0016226	0.0001249	652.7626	-12.9910281	0.0000000	12
Eagle	SUPER	AMR - EUR	0	0.0000572	0.0001107	652.7626	0.5169419	0.9856670	12
Eagle	SUPER	AMR - SAS	0	-0.0010397	0.0001185	652.7626	-8.7754908	0.0000000	12
Eagle	SUPER	EAS - EUR	0	0.0016798	0.0001308	652.7626	12.8432520	0.0000000	12
Eagle	SUPER	EAS - SAS	0	0.0005829	0.0001374	652.7626	4.2414451	0.0002456	12
Eagle	SUPER	EUR - SAS	0	-0.0010969	0.0001247	652.7626	-8.7983103	0.0000000	12
SHAPEIT	SUPER	AFR - AMR	0	-0.0005720	0.0000951	652.7626	-6.0165577	0.0000000	12
SHAPEIT	SUPER	AFR - EAS	0	-0.0019263	0.0001179	652.7626	-16.3450149	0.0000000	12
SHAPEIT	SUPER	AFR - EUR	0	-0.0004656	0.0001027	652.7626	-4.5341582	0.0000673	12
SHAPEIT	SUPER	AFR - SAS	0	-0.0015731	0.0001110	652.7626	-14.1702843	0.0000000	12
SHAPEIT	SUPER	AMR - EAS	0	-0.0013543	0.0001249	652.7626	-10.8432093	0.0000000	12
SHAPEIT	SUPER	AMR - EUR	0	0.0001064	0.0001107	652.7626	0.9608960	0.8725082	12
SHAPEIT	SUPER	AMR - SAS	0	-0.0010012	0.0001185	652.7626	-8.4507366	0.0000000	12
SHAPEIT	SUPER	EAS - EUR	0	0.0014607	0.0001308	652.7626	11.1679654	0.0000000	12
SHAPEIT	SUPER	EAS - SAS	0	0.0003531	0.0001374	652.7626	2.5694430	0.0772887	12
SHAPEIT	SUPER	EUR - SAS	0	-0.0011076	0.0001247	652.7626	-8.8839123	0.0000000	12
Beagle	SUPER	AFR - AMR	0	-0.0003963	0.0000674	660.9148	-5.8836425	0.0000001	13
Beagle	SUPER	AFR - EAS	0	-0.0018096	0.0000835	660.9148	-21.6699623	0.0000000	13
Beagle	SUPER	AFR - EUR	0	-0.0004075	0.0000728	660.9148	-5.6000461	0.0000003	13
Beagle	SUPER	AFR - SAS	0	-0.0012242	0.0000787	660.9148	-15.5626801	0.0000000	13
Beagle	SUPER	AMR - EAS	0	-0.0014133	0.0000885	660.9148	-15.9687917	0.0000000	13
Beagle	SUPER	AMR - EUR	0	-0.0000111	0.0000784	660.9148	-0.1419189	0.9999087	13
Beagle	SUPER	AMR - SAS	0	-0.0008279	0.0000839	660.9148	-9.8621509	0.0000000	13
Beagle	SUPER	EAS - EUR	0	0.0014021	0.0000927	660.9148	15.1291935	0.0000000	13
Beagle	SUPER	EAS - SAS	0	0.0005854	0.0000974	660.9148	6.0109070	0.0000000	13
Beagle	SUPER	EUR - SAS	0	-0.0008168	0.0000883	660.9148	-9.2459135	0.0000000	13
Eagle	SUPER	AFR - AMR	0	-0.0005377	0.0000674	660.9148	-7.9830149	0.0000000	13
Eagle	SUPER	AFR - EAS	0	-0.0022281	0.0000835	660.9148	-26.6819860	0.0000000	13
Eagle	SUPER	AFR - EUR	0	-0.0005174	0.0000728	660.9148	-7.1117186	0.0000000	13
Eagle	SUPER	AFR - SAS	0	-0.0015717	0.0000787	660.9148	-19.9798086	0.0000000	13
Eagle	SUPER	AMR - EAS	0	-0.0016904	0.0000885	660.9148	-19.1000713	0.0000000	13
Eagle	SUPER	AMR - EUR	0	0.0000203	0.0000784	660.9148	0.2587087	0.9990134	13
Eagle	SUPER	AMR - SAS	0	-0.0010340	0.0000839	660.9148	-12.3167330	0.0000000	13
Eagle	SUPER	EAS - EUR	0	0.0017107	0.0000927	660.9148	18.4584827	0.0000000	13
Eagle	SUPER	EAS - SAS	0	0.0006564	0.0000974	660.9148	6.7406680	0.0000000	13
Eagle	SUPER	EUR - SAS	0	-0.0010543	0.0000883	660.9148	-11.9342267	0.0000000	13
SHAPEIT	SUPER	AFR - AMR	0	-0.0004831	0.0000674	660.9148	-7.1713507	0.0000000	13
SHAPEIT	SUPER	AFR - EAS	0	-0.0018470	0.0000835	660.9148	-22.1178004	0.0000000	13
SHAPEIT	SUPER	AFR - EUR	0	-0.0004246	0.0000728	660.9148	-5.8358708	0.0000001	13
SHAPEIT	SUPER	AFR - SAS	0	-0.0013107	0.0000787	660.9148	-16.6615922	0.0000000	13
SHAPEIT	SUPER	AMR - EAS	0	-0.0013639	0.0000885	660.9148	-15.4112535	0.0000000	13
SHAPEIT	SUPER	AMR - EUR	0	0.0000584	0.0000784	660.9148	0.7451345	0.9457257	13
SHAPEIT	SUPER	AMR - SAS	0	-0.0008276	0.0000839	660.9148	-9.8586381	0.0000000	13
SHAPEIT	SUPER	EAS - EUR	0	0.0014224	0.0000927	660.9148	15.3475752	0.0000000	13
SHAPEIT	SUPER	EAS - SAS	0	0.0005363	0.0000974	660.9148	5.5072397	0.0000005	13
SHAPEIT	SUPER	EUR - SAS	0	-0.0008861	0.0000883	660.9148	-10.0302434	0.0000000	13
Beagle	SUPER	AFR - AMR	0	-0.0005153	0.0000781	653.1927	-6.6005741	0.0000000	14
Beagle	SUPER	AFR - EAS	0	-0.0018119	0.0000968	653.1927	-18.7223894	0.0000000	14
Beagle	SUPER	AFR - EUR	0	-0.0004380	0.0000843	653.1927	-5.1944788	0.0000027	14
Beagle	SUPER	AFR - SAS	0	-0.0013179	0.0000912	653.1927	-14.4556755	0.0000000	14
Beagle	SUPER	AMR - EAS	0	-0.0012966	0.0001026	653.1927	-12.6419026	0.0000000	14
Beagle	SUPER	AMR - EUR	0	0.0000773	0.0000909	653.1927	0.8499212	0.9147422	14
Beagle	SUPER	AMR - SAS	0	-0.0008026	0.0000973	653.1927	-8.2495488	0.0000000	14
Beagle	SUPER	EAS - EUR	0	0.0013739	0.0001074	653.1927	12.7916893	0.0000000	14
Beagle	SUPER	EAS - SAS	0	0.0004940	0.0001129	653.1927	4.3775452	0.0001359	14
Beagle	SUPER	EUR - SAS	0	-0.0008799	0.0001024	653.1927	-8.5941837	0.0000000	14
Eagle	SUPER	AFR - AMR	0	-0.0006659	0.0000781	653.1927	-8.5299660	0.0000000	14
Eagle	SUPER	AFR - EAS	0	-0.0022729	0.0000968	653.1927	-23.4850665	0.0000000	14
Eagle	SUPER	AFR - EUR	0	-0.0004992	0.0000843	653.1927	-5.9200570	0.0000001	14
Eagle	SUPER	AFR - SAS	0	-0.0015540	0.0000912	653.1927	-17.0458377	0.0000000	14
Eagle	SUPER	AMR - EAS	0	-0.0016070	0.0001026	653.1927	-15.6672839	0.0000000	14
Eagle	SUPER	AMR - EUR	0	0.0001667	0.0000909	653.1927	1.8337321	0.3549676	14
Eagle	SUPER	AMR - SAS	0	-0.0008881	0.0000973	653.1927	-9.1285414	0.0000000	14
Eagle	SUPER	EAS - EUR	0	0.0017737	0.0001074	653.1927	16.5134563	0.0000000	14
Eagle	SUPER	EAS - SAS	0	0.0007188	0.0001129	653.1927	6.3693024	0.0000000	14
Eagle	SUPER	EUR - SAS	0	-0.0010548	0.0001024	653.1927	-10.3030689	0.0000000	14
SHAPEIT	SUPER	AFR - AMR	0	-0.0006077	0.0000781	653.1927	-7.7846457	0.0000000	14
SHAPEIT	SUPER	AFR - EAS	0	-0.0019249	0.0000968	653.1927	-19.8899273	0.0000000	14
SHAPEIT	SUPER	AFR - EUR	0	-0.0004454	0.0000843	653.1927	-5.2814633	0.0000017	14
SHAPEIT	SUPER	AFR - SAS	0	-0.0013879	0.0000912	653.1927	-15.2233350	0.0000000	14
SHAPEIT	SUPER	AMR - EAS	0	-0.0013172	0.0001026	653.1927	-12.8423257	0.0000000	14
SHAPEIT	SUPER	AMR - EUR	0	0.0001624	0.0000909	653.1927	1.7860371	0.3825800	14
SHAPEIT	SUPER	AMR - SAS	0	-0.0007802	0.0000973	653.1927	-8.0187899	0.0000000	14
SHAPEIT	SUPER	EAS - EUR	0	0.0014796	0.0001074	653.1927	13.7754085	0.0000000	14
SHAPEIT	SUPER	EAS - SAS	0	0.0005371	0.0001129	653.1927	4.7586174	0.0000236	14
SHAPEIT	SUPER	EUR - SAS	0	-0.0009425	0.0001024	653.1927	-9.2061288	0.0000000	14
Beagle	SUPER	AFR - AMR	0	-0.0004353	0.0000914	656.1872	-4.7618899	0.0000233	15
Beagle	SUPER	AFR - EAS	0	-0.0021699	0.0001133	656.1872	-19.1473359	0.0000000	15
Beagle	SUPER	AFR - EUR	0	-0.0006028	0.0000987	656.1872	-6.1052685	0.0000000	15
Beagle	SUPER	AFR - SAS	0	-0.0015207	0.0001068	656.1872	-14.2444128	0.0000000	15
Beagle	SUPER	AMR - EAS	0	-0.0017346	0.0001201	656.1872	-14.4423262	0.0000000	15
Beagle	SUPER	AMR - EUR	0	-0.0001675	0.0001065	656.1872	-1.5738279	0.5147790	15
Beagle	SUPER	AMR - SAS	0	-0.0010854	0.0001139	656.1872	-9.5269507	0.0000000	15
Beagle	SUPER	EAS - EUR	0	0.0015670	0.0001258	656.1872	12.4595392	0.0000000	15
Beagle	SUPER	EAS - SAS	0	0.0006492	0.0001322	656.1872	4.9126013	0.0000112	15
Beagle	SUPER	EUR - SAS	0	-0.0009178	0.0001199	656.1872	-7.6558970	0.0000000	15
Eagle	SUPER	AFR - AMR	0	-0.0004916	0.0000914	656.1872	-5.3780183	0.0000010	15
Eagle	SUPER	AFR - EAS	0	-0.0025493	0.0001133	656.1872	-22.4952292	0.0000000	15
Eagle	SUPER	AFR - EUR	0	-0.0005827	0.0000987	656.1872	-5.9014491	0.0000001	15
Eagle	SUPER	AFR - SAS	0	-0.0018062	0.0001068	656.1872	-16.9190560	0.0000000	15
Eagle	SUPER	AMR - EAS	0	-0.0020577	0.0001201	656.1872	-17.1323231	0.0000000	15
Eagle	SUPER	AMR - EUR	0	-0.0000911	0.0001065	656.1872	-0.8556841	0.9127880	15
Eagle	SUPER	AMR - SAS	0	-0.0013146	0.0001139	656.1872	-11.5388757	0.0000000	15
Eagle	SUPER	EAS - EUR	0	0.0019666	0.0001258	656.1872	15.6361726	0.0000000	15
Eagle	SUPER	EAS - SAS	0	0.0007431	0.0001322	656.1872	5.6229133	0.0000003	15
Eagle	SUPER	EUR - SAS	0	-0.0012235	0.0001199	656.1872	-10.2054981	0.0000000	15
SHAPEIT	SUPER	AFR - AMR	0	-0.0005581	0.0000914	656.1872	-6.1051462	0.0000000	15
SHAPEIT	SUPER	AFR - EAS	0	-0.0022967	0.0001133	656.1872	-20.2663472	0.0000000	15
SHAPEIT	SUPER	AFR - EUR	0	-0.0006185	0.0000987	656.1872	-6.2636999	0.0000000	15
SHAPEIT	SUPER	AFR - SAS	0	-0.0016815	0.0001068	656.1872	-15.7515208	0.0000000	15
SHAPEIT	SUPER	AMR - EAS	0	-0.0017386	0.0001201	656.1872	-14.4758028	0.0000000	15
SHAPEIT	SUPER	AMR - EUR	0	-0.0000604	0.0001065	656.1872	-0.5672865	0.9797282	15
SHAPEIT	SUPER	AMR - SAS	0	-0.0011234	0.0001139	656.1872	-9.8613710	0.0000000	15
SHAPEIT	SUPER	EAS - EUR	0	0.0016782	0.0001258	656.1872	13.3434417	0.0000000	15
SHAPEIT	SUPER	EAS - SAS	0	0.0006151	0.0001322	656.1872	4.6547380	0.0000386	15
SHAPEIT	SUPER	EUR - SAS	0	-0.0010631	0.0001199	656.1872	-8.8674629	0.0000000	15
Beagle	SUPER	AFR - AMR	0	-0.0006495	0.0000979	653.4378	-6.6332752	0.0000000	16
Beagle	SUPER	AFR - EAS	0	-0.0023399	0.0001214	653.4378	-19.2755192	0.0000000	16
Beagle	SUPER	AFR - EUR	0	-0.0005213	0.0001058	653.4378	-4.9284923	0.0000104	16
Beagle	SUPER	AFR - SAS	0	-0.0016488	0.0001144	653.4378	-14.4187146	0.0000000	16
Beagle	SUPER	AMR - EAS	0	-0.0016904	0.0001287	653.4378	-13.1389254	0.0000000	16
Beagle	SUPER	AMR - EUR	0	0.0001283	0.0001140	653.4378	1.1247215	0.7934607	16
Beagle	SUPER	AMR - SAS	0	-0.0009993	0.0001220	653.4378	-8.1886747	0.0000000	16
Beagle	SUPER	EAS - EUR	0	0.0018186	0.0001347	653.4378	13.4989089	0.0000000	16
Beagle	SUPER	EAS - SAS	0	0.0006911	0.0001416	653.4378	4.8817205	0.0000131	16
Beagle	SUPER	EUR - SAS	0	-0.0011276	0.0001284	653.4378	-8.7803472	0.0000000	16
Eagle	SUPER	AFR - AMR	0	-0.0006846	0.0000979	653.4378	-6.9910749	0.0000000	16
Eagle	SUPER	AFR - EAS	0	-0.0027536	0.0001214	653.4378	-22.6835873	0.0000000	16
Eagle	SUPER	AFR - EUR	0	-0.0006338	0.0001058	653.4378	-5.9920944	0.0000000	16
Eagle	SUPER	AFR - SAS	0	-0.0017238	0.0001144	653.4378	-15.0738891	0.0000000	16
Eagle	SUPER	AMR - EAS	0	-0.0020691	0.0001287	653.4378	-16.0823202	0.0000000	16
Eagle	SUPER	AMR - EUR	0	0.0000508	0.0001140	653.4378	0.4454190	0.9918448	16
Eagle	SUPER	AMR - SAS	0	-0.0010392	0.0001220	653.4378	-8.5155143	0.0000000	16
Eagle	SUPER	EAS - EUR	0	0.0021198	0.0001347	653.4378	15.7347283	0.0000000	16
Eagle	SUPER	EAS - SAS	0	0.0010299	0.0001416	653.4378	7.2749511	0.0000000	16
Eagle	SUPER	EUR - SAS	0	-0.0010900	0.0001284	653.4378	-8.4877471	0.0000000	16
SHAPEIT	SUPER	AFR - AMR	0	-0.0007895	0.0000979	653.4378	-8.0622376	0.0000000	16
SHAPEIT	SUPER	AFR - EAS	0	-0.0025396	0.0001214	653.4378	-20.9205306	0.0000000	16
SHAPEIT	SUPER	AFR - EUR	0	-0.0006761	0.0001058	653.4378	-6.3923138	0.0000000	16
SHAPEIT	SUPER	AFR - SAS	0	-0.0017614	0.0001144	653.4378	-15.4030212	0.0000000	16
SHAPEIT	SUPER	AMR - EAS	0	-0.0017501	0.0001287	653.4378	-13.6034830	0.0000000	16
SHAPEIT	SUPER	AMR - EUR	0	0.0001133	0.0001140	653.4378	0.9940318	0.8580562	16
SHAPEIT	SUPER	AMR - SAS	0	-0.0009719	0.0001220	653.4378	-7.9644262	0.0000000	16
SHAPEIT	SUPER	EAS - EUR	0	0.0018635	0.0001347	653.4378	13.8319203	0.0000000	16
SHAPEIT	SUPER	EAS - SAS	0	0.0007782	0.0001416	653.4378	5.4972279	0.0000006	16
SHAPEIT	SUPER	EUR - SAS	0	-0.0010853	0.0001284	653.4378	-8.4511982	0.0000000	16
Beagle	SUPER	AFR - AMR	0	-0.0006515	0.0001001	650.1826	-6.5071736	0.0000000	17
Beagle	SUPER	AFR - EAS	0	-0.0026169	0.0001241	650.1826	-21.0828180	0.0000000	17
Beagle	SUPER	AFR - EUR	0	-0.0006443	0.0001081	650.1826	-5.9577574	0.0000000	17
Beagle	SUPER	AFR - SAS	0	-0.0018114	0.0001169	650.1826	-15.4919024	0.0000000	17
Beagle	SUPER	AMR - EAS	0	-0.0019654	0.0001315	650.1826	-14.9402023	0.0000000	17
Beagle	SUPER	AMR - EUR	0	0.0000072	0.0001166	650.1826	0.0617274	0.9999967	17
Beagle	SUPER	AMR - SAS	0	-0.0011599	0.0001248	650.1826	-9.2955037	0.0000000	17
Beagle	SUPER	EAS - EUR	0	0.0019726	0.0001378	650.1826	14.3193133	0.0000000	17
Beagle	SUPER	EAS - SAS	0	0.0008055	0.0001447	650.1826	5.5645944	0.0000004	17
Beagle	SUPER	EUR - SAS	0	-0.0011671	0.0001313	650.1826	-8.8882625	0.0000000	17
Eagle	SUPER	AFR - AMR	0	-0.0007019	0.0001001	650.1826	-7.0100132	0.0000000	17
Eagle	SUPER	AFR - EAS	0	-0.0029560	0.0001241	650.1826	-23.8146589	0.0000000	17
Eagle	SUPER	AFR - EUR	0	-0.0006728	0.0001081	650.1826	-6.2209768	0.0000000	17
Eagle	SUPER	AFR - SAS	0	-0.0020983	0.0001169	650.1826	-17.9452459	0.0000000	17
Eagle	SUPER	AMR - EAS	0	-0.0022541	0.0001315	650.1826	-17.1351420	0.0000000	17
Eagle	SUPER	AMR - EUR	0	0.0000291	0.0001166	650.1826	0.2493794	0.9991463	17
Eagle	SUPER	AMR - SAS	0	-0.0013964	0.0001248	650.1826	-11.1909603	0.0000000	17
Eagle	SUPER	EAS - EUR	0	0.0022832	0.0001378	650.1826	16.5741875	0.0000000	17
Eagle	SUPER	EAS - SAS	0	0.0008577	0.0001447	650.1826	5.9253957	0.0000000	17
Eagle	SUPER	EUR - SAS	0	-0.0014255	0.0001313	650.1826	-10.8561290	0.0000000	17
SHAPEIT	SUPER	AFR - AMR	0	-0.0006865	0.0001001	650.1826	-6.8567863	0.0000000	17
SHAPEIT	SUPER	AFR - EAS	0	-0.0027376	0.0001241	650.1826	-22.0556858	0.0000000	17
SHAPEIT	SUPER	AFR - EUR	0	-0.0006403	0.0001081	650.1826	-5.9202583	0.0000001	17
SHAPEIT	SUPER	AFR - SAS	0	-0.0017637	0.0001169	650.1826	-15.0835378	0.0000000	17
SHAPEIT	SUPER	AMR - EAS	0	-0.0020511	0.0001315	650.1826	-15.5920660	0.0000000	17
SHAPEIT	SUPER	AMR - EUR	0	0.0000463	0.0001166	650.1826	0.3967336	0.9947687	17
SHAPEIT	SUPER	AMR - SAS	0	-0.0010771	0.0001248	650.1826	-8.6323095	0.0000000	17
SHAPEIT	SUPER	EAS - EUR	0	0.0020974	0.0001378	650.1826	15.2253554	0.0000000	17
SHAPEIT	SUPER	EAS - SAS	0	0.0009740	0.0001447	650.1826	6.7287206	0.0000000	17
SHAPEIT	SUPER	EUR - SAS	0	-0.0011234	0.0001313	650.1826	-8.5555059	0.0000000	17
Beagle	SUPER	AFR - AMR	0	-0.0005757	0.0000783	663.0280	-7.3518272	0.0000000	18
Beagle	SUPER	AFR - EAS	0	-0.0021172	0.0000971	663.0280	-21.8100354	0.0000000	18
Beagle	SUPER	AFR - EUR	0	-0.0005734	0.0000846	663.0280	-6.7792484	0.0000000	18
Beagle	SUPER	AFR - SAS	0	-0.0014635	0.0000914	663.0280	-16.0042708	0.0000000	18
Beagle	SUPER	AMR - EAS	0	-0.0015415	0.0001029	663.0280	-14.9834938	0.0000000	18
Beagle	SUPER	AMR - EUR	0	0.0000023	0.0000912	663.0280	0.0250746	0.9999999	18
Beagle	SUPER	AMR - SAS	0	-0.0008878	0.0000976	663.0280	-9.0978713	0.0000000	18
Beagle	SUPER	EAS - EUR	0	0.0015438	0.0001077	663.0280	14.3296314	0.0000000	18
Beagle	SUPER	EAS - SAS	0	0.0006537	0.0001132	663.0280	5.7743071	0.0000001	18
Beagle	SUPER	EUR - SAS	0	-0.0008901	0.0001027	663.0280	-8.6679076	0.0000000	18
Eagle	SUPER	AFR - AMR	0	-0.0006346	0.0000783	663.0280	-8.1041081	0.0000000	18
Eagle	SUPER	AFR - EAS	0	-0.0025268	0.0000971	663.0280	-26.0298431	0.0000000	18
Eagle	SUPER	AFR - EUR	0	-0.0006685	0.0000846	663.0280	-7.9039036	0.0000000	18
Eagle	SUPER	AFR - SAS	0	-0.0016961	0.0000914	663.0280	-18.5480253	0.0000000	18
Eagle	SUPER	AMR - EAS	0	-0.0018922	0.0001029	663.0280	-18.3925675	0.0000000	18
Eagle	SUPER	AMR - EUR	0	-0.0000339	0.0000912	663.0280	-0.3721051	0.9959161	18
Eagle	SUPER	AMR - SAS	0	-0.0010615	0.0000976	663.0280	-10.8778961	0.0000000	18
Eagle	SUPER	EAS - EUR	0	0.0018583	0.0001077	663.0280	17.2489364	0.0000000	18
Eagle	SUPER	EAS - SAS	0	0.0008307	0.0001132	663.0280	7.3380322	0.0000000	18
Eagle	SUPER	EUR - SAS	0	-0.0010276	0.0001027	663.0280	-10.0067727	0.0000000	18
SHAPEIT	SUPER	AFR - AMR	0	-0.0006185	0.0000783	663.0280	-7.8983140	0.0000000	18
SHAPEIT	SUPER	AFR - EAS	0	-0.0022082	0.0000971	663.0280	-22.7481024	0.0000000	18
SHAPEIT	SUPER	AFR - EUR	0	-0.0006070	0.0000846	663.0280	-7.1761223	0.0000000	18
SHAPEIT	SUPER	AFR - SAS	0	-0.0014875	0.0000914	663.0280	-16.2661910	0.0000000	18
SHAPEIT	SUPER	AMR - EAS	0	-0.0015898	0.0001029	663.0280	-15.4526759	0.0000000	18
SHAPEIT	SUPER	AMR - EUR	0	0.0000115	0.0000912	663.0280	0.1262350	0.9999427	18
SHAPEIT	SUPER	AMR - SAS	0	-0.0008690	0.0000976	663.0280	-8.9048037	0.0000000	18
SHAPEIT	SUPER	EAS - EUR	0	0.0016013	0.0001077	663.0280	14.8632962	0.0000000	18
SHAPEIT	SUPER	EAS - SAS	0	0.0007208	0.0001132	663.0280	6.3671379	0.0000000	18
SHAPEIT	SUPER	EUR - SAS	0	-0.0008805	0.0001027	663.0280	-8.5742632	0.0000000	18
Beagle	SUPER	AFR - AMR	0	-0.0005653	0.0000918	666.2443	-6.1554178	0.0000000	19
Beagle	SUPER	AFR - EAS	0	-0.0024086	0.0001139	666.2443	-21.1560070	0.0000000	19
Beagle	SUPER	AFR - EUR	0	-0.0005226	0.0000992	666.2443	-5.2684408	0.0000018	19
Beagle	SUPER	AFR - SAS	0	-0.0015580	0.0001072	666.2443	-14.5267846	0.0000000	19
Beagle	SUPER	AMR - EAS	0	-0.0018433	0.0001207	666.2443	-15.2769893	0.0000000	19
Beagle	SUPER	AMR - EUR	0	0.0000427	0.0001069	666.2443	0.3990473	0.9946505	19
Beagle	SUPER	AMR - SAS	0	-0.0009927	0.0001145	666.2443	-8.6733780	0.0000000	19
Beagle	SUPER	EAS - EUR	0	0.0018860	0.0001264	666.2443	14.9264329	0.0000000	19
Beagle	SUPER	EAS - SAS	0	0.0008506	0.0001328	666.2443	6.4069730	0.0000000	19
Beagle	SUPER	EUR - SAS	0	-0.0010354	0.0001204	666.2443	-8.5965874	0.0000000	19
Eagle	SUPER	AFR - AMR	0	-0.0005826	0.0000918	666.2443	-6.3439089	0.0000000	19
Eagle	SUPER	AFR - EAS	0	-0.0027000	0.0001139	666.2443	-23.7153871	0.0000000	19
Eagle	SUPER	AFR - EUR	0	-0.0005104	0.0000992	666.2443	-5.1449956	0.0000035	19
Eagle	SUPER	AFR - SAS	0	-0.0016569	0.0001072	666.2443	-15.4490484	0.0000000	19
Eagle	SUPER	AMR - EAS	0	-0.0021174	0.0001207	666.2443	-17.5484586	0.0000000	19
Eagle	SUPER	AMR - EUR	0	0.0000722	0.0001069	666.2443	0.6754135	0.9616864	19
Eagle	SUPER	AMR - SAS	0	-0.0010743	0.0001145	666.2443	-9.3863511	0.0000000	19
Eagle	SUPER	EAS - EUR	0	0.0021896	0.0001264	666.2443	17.3294761	0.0000000	19
Eagle	SUPER	EAS - SAS	0	0.0010431	0.0001328	666.2443	7.8566854	0.0000000	19
Eagle	SUPER	EUR - SAS	0	-0.0011465	0.0001204	666.2443	-9.5195229	0.0000000	19
SHAPEIT	SUPER	AFR - AMR	0	-0.0006047	0.0000918	666.2443	-6.5850303	0.0000000	19
SHAPEIT	SUPER	AFR - EAS	0	-0.0025295	0.0001139	666.2443	-22.2178152	0.0000000	19
SHAPEIT	SUPER	AFR - EUR	0	-0.0005555	0.0000992	666.2443	-5.6002953	0.0000003	19
SHAPEIT	SUPER	AFR - SAS	0	-0.0016702	0.0001072	666.2443	-15.5734930	0.0000000	19
SHAPEIT	SUPER	AMR - EAS	0	-0.0019248	0.0001207	666.2443	-15.9518841	0.0000000	19
SHAPEIT	SUPER	AMR - EUR	0	0.0000492	0.0001069	666.2443	0.4601536	0.9907685	19
SHAPEIT	SUPER	AMR - SAS	0	-0.0010655	0.0001145	666.2443	-9.3094866	0.0000000	19
SHAPEIT	SUPER	EAS - EUR	0	0.0019740	0.0001264	666.2443	15.6226404	0.0000000	19
SHAPEIT	SUPER	EAS - SAS	0	0.0008593	0.0001328	666.2443	6.4719657	0.0000000	19
SHAPEIT	SUPER	EUR - SAS	0	-0.0011147	0.0001204	666.2443	-9.2553370	0.0000000	19
Beagle	SUPER	AFR - AMR	0	-0.0007722	0.0001025	652.0675	-7.5365726	0.0000000	20
Beagle	SUPER	AFR - EAS	0	-0.0027695	0.0001270	652.0675	-21.8029830	0.0000000	20
Beagle	SUPER	AFR - EUR	0	-0.0005905	0.0001107	652.0675	-5.3355198	0.0000013	20
Beagle	SUPER	AFR - SAS	0	-0.0017334	0.0001197	652.0675	-14.4864655	0.0000000	20
Beagle	SUPER	AMR - EAS	0	-0.0019973	0.0001346	652.0675	-14.8362259	0.0000000	20
Beagle	SUPER	AMR - EUR	0	0.0001817	0.0001193	652.0675	1.5228683	0.5479119	20
Beagle	SUPER	AMR - SAS	0	-0.0009612	0.0001277	652.0675	-7.5273517	0.0000000	20
Beagle	SUPER	EAS - EUR	0	0.0021790	0.0001410	652.0675	15.4567275	0.0000000	20
Beagle	SUPER	EAS - SAS	0	0.0010361	0.0001481	652.0675	6.9943358	0.0000000	20
Beagle	SUPER	EUR - SAS	0	-0.0011429	0.0001344	652.0675	-8.5054351	0.0000000	20
Eagle	SUPER	AFR - AMR	0	-0.0008697	0.0001025	652.0675	-8.4874557	0.0000000	20
Eagle	SUPER	AFR - EAS	0	-0.0030693	0.0001270	652.0675	-24.1633525	0.0000000	20
Eagle	SUPER	AFR - EUR	0	-0.0005752	0.0001107	652.0675	-5.1973791	0.0000027	20
Eagle	SUPER	AFR - SAS	0	-0.0019132	0.0001197	652.0675	-15.9888272	0.0000000	20
Eagle	SUPER	AMR - EAS	0	-0.0021997	0.0001346	652.0675	-16.3396442	0.0000000	20
Eagle	SUPER	AMR - EUR	0	0.0002944	0.0001193	652.0675	2.4675553	0.0993608	20
Eagle	SUPER	AMR - SAS	0	-0.0010435	0.0001277	652.0675	-8.1721665	0.0000000	20
Eagle	SUPER	EAS - EUR	0	0.0024941	0.0001410	652.0675	17.6919896	0.0000000	20
Eagle	SUPER	EAS - SAS	0	0.0011561	0.0001481	652.0675	7.8047927	0.0000000	20
Eagle	SUPER	EUR - SAS	0	-0.0013380	0.0001344	652.0675	-9.9570424	0.0000000	20
SHAPEIT	SUPER	AFR - AMR	0	-0.0008548	0.0001025	652.0675	-8.3429085	0.0000000	20
SHAPEIT	SUPER	AFR - EAS	0	-0.0028661	0.0001270	652.0675	-22.5636566	0.0000000	20
SHAPEIT	SUPER	AFR - EUR	0	-0.0006142	0.0001107	652.0675	-5.5490767	0.0000004	20
SHAPEIT	SUPER	AFR - SAS	0	-0.0017982	0.0001197	652.0675	-15.0279595	0.0000000	20
SHAPEIT	SUPER	AMR - EAS	0	-0.0020113	0.0001346	652.0675	-14.9402499	0.0000000	20
SHAPEIT	SUPER	AMR - EUR	0	0.0002407	0.0001193	652.0675	2.0172070	0.2588100	20
SHAPEIT	SUPER	AMR - SAS	0	-0.0009434	0.0001277	652.0675	-7.3877582	0.0000000	20
SHAPEIT	SUPER	EAS - EUR	0	0.0022520	0.0001410	652.0675	15.9744717	0.0000000	20
SHAPEIT	SUPER	EAS - SAS	0	0.0010679	0.0001481	652.0675	7.2092102	0.0000000	20
SHAPEIT	SUPER	EUR - SAS	0	-0.0011841	0.0001344	652.0675	-8.8117335	0.0000000	20
Beagle	SUPER	AFR - AMR	0	-0.0002164	0.0000976	696.3982	-2.2165641	0.1747130	21
Beagle	SUPER	AFR - EAS	0	-0.0016942	0.0001210	696.3982	-13.9967600	0.0000000	21
Beagle	SUPER	AFR - EUR	0	-0.0001822	0.0001055	696.3982	-1.7276072	0.4175899	21
Beagle	SUPER	AFR - SAS	0	-0.0011539	0.0001140	696.3982	-10.1199434	0.0000000	21
Beagle	SUPER	AMR - EAS	0	-0.0014778	0.0001283	696.3982	-11.5197383	0.0000000	21
Beagle	SUPER	AMR - EUR	0	0.0000342	0.0001137	696.3982	0.3009711	0.9982130	21
Beagle	SUPER	AMR - SAS	0	-0.0009375	0.0001217	696.3982	-7.7044437	0.0000000	21
Beagle	SUPER	EAS - EUR	0	0.0015120	0.0001343	696.3982	11.2554544	0.0000000	21
Beagle	SUPER	EAS - SAS	0	0.0005403	0.0001412	696.3982	3.8276206	0.0013258	21
Beagle	SUPER	EUR - SAS	0	-0.0009717	0.0001280	696.3982	-7.5887283	0.0000000	21
Eagle	SUPER	AFR - AMR	0	-0.0002526	0.0000976	696.3982	-2.5873233	0.0737863	21
Eagle	SUPER	AFR - EAS	0	-0.0020187	0.0001210	696.3982	-16.6779455	0.0000000	21
Eagle	SUPER	AFR - EUR	0	-0.0002613	0.0001055	696.3982	-2.4777356	0.0968707	21
Eagle	SUPER	AFR - SAS	0	-0.0013512	0.0001140	696.3982	-11.8505178	0.0000000	21
Eagle	SUPER	AMR - EAS	0	-0.0017661	0.0001283	696.3982	-13.7674105	0.0000000	21
Eagle	SUPER	AMR - EUR	0	-0.0000087	0.0001137	696.3982	-0.0764366	0.9999923	21
Eagle	SUPER	AMR - SAS	0	-0.0010986	0.0001217	696.3982	-9.0286020	0.0000000	21
Eagle	SUPER	EAS - EUR	0	0.0017574	0.0001343	696.3982	13.0824203	0.0000000	21
Eagle	SUPER	EAS - SAS	0	0.0006675	0.0001412	696.3982	4.7288336	0.0000269	21
Eagle	SUPER	EUR - SAS	0	-0.0010899	0.0001280	696.3982	-8.5119437	0.0000000	21
SHAPEIT	SUPER	AFR - AMR	0	-0.0003551	0.0000976	696.3982	-3.6365712	0.0027379	21
SHAPEIT	SUPER	AFR - EAS	0	-0.0017594	0.0001210	696.3982	-14.5360105	0.0000000	21
SHAPEIT	SUPER	AFR - EUR	0	-0.0002181	0.0001055	696.3982	-2.0678150	0.2353156	21
SHAPEIT	SUPER	AFR - SAS	0	-0.0012626	0.0001140	696.3982	-11.0732426	0.0000000	21
SHAPEIT	SUPER	AMR - EAS	0	-0.0014044	0.0001283	696.3982	-10.9477579	0.0000000	21
SHAPEIT	SUPER	AMR - EUR	0	0.0001370	0.0001137	696.3982	1.2048120	0.7486242	21
SHAPEIT	SUPER	AMR - SAS	0	-0.0009075	0.0001217	696.3982	-7.4583250	0.0000000	21
SHAPEIT	SUPER	EAS - EUR	0	0.0015414	0.0001343	696.3982	11.4742535	0.0000000	21
SHAPEIT	SUPER	EAS - SAS	0	0.0004969	0.0001412	696.3982	3.5199665	0.0041855	21
SHAPEIT	SUPER	EUR - SAS	0	-0.0010445	0.0001280	696.3982	-8.1574183	0.0000000	21
Beagle	SUPER	AFR - AMR	0	-0.0004068	0.0001265	677.1751	-3.2154756	0.0118738	22
Beagle	SUPER	AFR - EAS	0	-0.0025320	0.0001568	677.1751	-16.1443411	0.0000000	22
Beagle	SUPER	AFR - EUR	0	-0.0005019	0.0001366	677.1751	-3.6726859	0.0023985	22
Beagle	SUPER	AFR - SAS	0	-0.0016743	0.0001477	677.1751	-11.3328909	0.0000000	22
Beagle	SUPER	AMR - EAS	0	-0.0021252	0.0001662	677.1751	-12.7858221	0.0000000	22
Beagle	SUPER	AMR - EUR	0	-0.0000951	0.0001473	677.1751	-0.6454124	0.9674745	22
Beagle	SUPER	AMR - SAS	0	-0.0012675	0.0001577	677.1751	-8.0395209	0.0000000	22
Beagle	SUPER	EAS - EUR	0	0.0020301	0.0001741	677.1751	11.6634779	0.0000000	22
Beagle	SUPER	EAS - SAS	0	0.0008577	0.0001829	677.1751	4.6893952	0.0000326	22
Beagle	SUPER	EUR - SAS	0	-0.0011724	0.0001659	677.1751	-7.0667990	0.0000000	22
Eagle	SUPER	AFR - AMR	0	-0.0004200	0.0001265	677.1751	-3.3196563	0.0084076	22
Eagle	SUPER	AFR - EAS	0	-0.0028060	0.0001568	677.1751	-17.8915712	0.0000000	22
Eagle	SUPER	AFR - EUR	0	-0.0004205	0.0001366	677.1751	-3.0770329	0.0184482	22
Eagle	SUPER	AFR - SAS	0	-0.0017566	0.0001477	677.1751	-11.8900892	0.0000000	22
Eagle	SUPER	AMR - EAS	0	-0.0023860	0.0001662	677.1751	-14.3551479	0.0000000	22
Eagle	SUPER	AMR - EUR	0	-0.0000005	0.0001473	677.1751	-0.0034443	1.0000000	22
Eagle	SUPER	AMR - SAS	0	-0.0013367	0.0001577	677.1751	-8.4780557	0.0000000	22
Eagle	SUPER	EAS - EUR	0	0.0023855	0.0001741	677.1751	13.7054575	0.0000000	22
Eagle	SUPER	EAS - SAS	0	0.0010494	0.0001829	677.1751	5.7375731	0.0000001	22
Eagle	SUPER	EUR - SAS	0	-0.0013362	0.0001659	677.1751	-8.0535776	0.0000000	22
SHAPEIT	SUPER	AFR - AMR	0	-0.0005374	0.0001265	677.1751	-4.2480443	0.0002377	22
SHAPEIT	SUPER	AFR - EAS	0	-0.0025975	0.0001568	677.1751	-16.5620008	0.0000000	22
SHAPEIT	SUPER	AFR - EUR	0	-0.0006499	0.0001366	677.1751	-4.7556728	0.0000238	22
SHAPEIT	SUPER	AFR - SAS	0	-0.0017755	0.0001477	677.1751	-12.0175142	0.0000000	22
SHAPEIT	SUPER	AMR - EAS	0	-0.0020601	0.0001662	677.1751	-12.3940007	0.0000000	22
SHAPEIT	SUPER	AMR - EUR	0	-0.0001124	0.0001473	677.1751	-0.7632502	0.9409835	22
SHAPEIT	SUPER	AMR - SAS	0	-0.0012380	0.0001577	677.1751	-7.8525184	0.0000000	22
SHAPEIT	SUPER	EAS - EUR	0	0.0019476	0.0001741	677.1751	11.1895725	0.0000000	22
SHAPEIT	SUPER	EAS - SAS	0	0.0008220	0.0001829	677.1751	4.4945101	0.0000801	22
SHAPEIT	SUPER	EUR - SAS	0	-0.0011256	0.0001659	677.1751	-6.7844566	0.0000000	22
Beagle	SUPER	AFR - AMR	0	-0.0003326	0.0000593	1089.0700	-5.6083028	0.0000003	23
Beagle	SUPER	AFR - EAS	0	-0.0019472	0.0000593	1089.0700	-32.8312056	0.0000000	23
Beagle	SUPER	AFR - EUR	0	-0.0006228	0.0000593	1089.0700	-10.5014284	0.0000000	23
Beagle	SUPER	AFR - SAS	0	-0.0011571	0.0000593	1089.0700	-19.5101249	0.0000000	23
Beagle	SUPER	AMR - EAS	0	-0.0016146	0.0000593	1089.0700	-27.2229028	0.0000000	23
Beagle	SUPER	AMR - EUR	0	-0.0002902	0.0000593	1089.0700	-4.8931256	0.0000113	23
Beagle	SUPER	AMR - SAS	0	-0.0008245	0.0000593	1089.0700	-13.9018222	0.0000000	23
Beagle	SUPER	EAS - EUR	0	0.0013244	0.0000593	1089.0700	22.3297772	0.0000000	23
Beagle	SUPER	EAS - SAS	0	0.0007901	0.0000593	1089.0700	13.3210806	0.0000000	23
Beagle	SUPER	EUR - SAS	0	-0.0005343	0.0000593	1089.0700	-9.0086966	0.0000000	23
Eagle	SUPER	AFR - AMR	0	-0.0003202	0.0000593	1089.0700	-5.3985365	0.0000008	23
Eagle	SUPER	AFR - EAS	0	-0.0023056	0.0000593	1089.0700	-38.8734268	0.0000000	23
Eagle	SUPER	AFR - EUR	0	-0.0007077	0.0000593	1089.0700	-11.9330217	0.0000000	23
Eagle	SUPER	AFR - SAS	0	-0.0013356	0.0000593	1089.0700	-22.5189925	0.0000000	23
Eagle	SUPER	AMR - EAS	0	-0.0019854	0.0000593	1089.0700	-33.4748903	0.0000000	23
Eagle	SUPER	AMR - EUR	0	-0.0003876	0.0000593	1089.0700	-6.5344852	0.0000000	23
Eagle	SUPER	AMR - SAS	0	-0.0010154	0.0000593	1089.0700	-17.1204559	0.0000000	23
Eagle	SUPER	EAS - EUR	0	0.0015978	0.0000593	1089.0700	26.9404051	0.0000000	23
Eagle	SUPER	EAS - SAS	0	0.0009700	0.0000593	1089.0700	16.3544343	0.0000000	23
Eagle	SUPER	EUR - SAS	0	-0.0006278	0.0000593	1089.0700	-10.5859707	0.0000000	23
SHAPEIT	SUPER	AFR - AMR	0	-0.0003732	0.0000593	1089.0700	-6.2929479	0.0000000	23
SHAPEIT	SUPER	AFR - EAS	0	-0.0018829	0.0000593	1089.0700	-31.7473628	0.0000000	23
SHAPEIT	SUPER	AFR - EUR	0	-0.0006244	0.0000593	1089.0700	-10.5276276	0.0000000	23
SHAPEIT	SUPER	AFR - SAS	0	-0.0010932	0.0000593	1089.0700	-18.4315950	0.0000000	23
SHAPEIT	SUPER	AMR - EAS	0	-0.0015097	0.0000593	1089.0700	-25.4544149	0.0000000	23
SHAPEIT	SUPER	AMR - EUR	0	-0.0002512	0.0000593	1089.0700	-4.2346797	0.0002401	23
SHAPEIT	SUPER	AMR - SAS	0	-0.0007199	0.0000593	1089.0700	-12.1386471	0.0000000	23
SHAPEIT	SUPER	EAS - EUR	0	0.0012585	0.0000593	1089.0700	21.2197352	0.0000000	23
SHAPEIT	SUPER	EAS - SAS	0	0.0007898	0.0000593	1089.0700	13.3157679	0.0000000	23
SHAPEIT	SUPER	EUR - SAS	0	-0.0004688	0.0000593	1089.0700	-7.9039673	0.0000000	23

Flip Errors

# df_flips <- df_switch_trio[[1]] %>%
#   mutate(Eagle = (n_flip_eagle) / n_hets,
#          Beagle = (n_flip_beagle) / n_hets,
#          SHAPEIT = (n_flip_shapeit) / n_hets) %>%
#   select(Eagle, Beagle, SHAPEIT, SUPER, pair_id) %>%
#   mutate(chrom = 1)
# 
# for(i in 2:22){
#   df_flips <- bind_rows(df_flips, 
#                         {
#                           df_switch_trio[[i]] %>%
#                             mutate(Eagle = (n_flip_eagle) / n_hets,
#                                    Beagle = (n_flip_beagle) / n_hets,
#                                    SHAPEIT = (n_flip_shapeit) / n_hets) %>%
#                             select(Eagle, Beagle, SHAPEIT, SUPER, pair_id) %>%
#                             mutate(chrom = i)
#                         })
# }

df_flips <- df_switch_trio_noth %>%
  mutate(Eagle = (n_flip_e) / n_het,
         Beagle = (n_flip_b) / n_het,
         SHAPEIT = (n_flip_s) / n_het) %>%
  select(Eagle, Beagle, SHAPEIT, sample, chrom)

df_flips <- df_flips %>%
  left_join({df_subj_rel %>% select(id2, SUPER)}, by = c("sample" = "id2")) %>%
  rename(pair_id = sample) %>%
  select(Eagle, Beagle, SHAPEIT, SUPER, pair_id, chrom)

df_flips <- df_flips %>%
  bind_rows({df_switch_x %>%
      mutate(Eagle = (n_flip_eagle) / n_hets,
             Beagle = (n_flip_beagle) / n_hets,
             SHAPEIT = (n_flip_shapeit) / n_hets) %>%
      rename(SUPER = pop) %>%
                            select(Eagle, Beagle, SHAPEIT, SUPER) %>%
                            mutate(pair_id = 603:1602, chrom = 23)})

df_flips %>%
  group_by(chrom) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>% 
  knitr::kable()

chrom	Beagle	Eagle	SHAPEIT
1	0.0057436	0.0049992	0.0062407
2	0.0058785	0.0050772	0.0064003
3	0.0055282	0.0047878	0.0060123
4	0.0052003	0.0045228	0.0056534
5	0.0055357	0.0048034	0.0060346
6	0.0050140	0.0043553	0.0054361
7	0.0055456	0.0048417	0.0060457
8	0.0055975	0.0048655	0.0061065
9	0.0061151	0.0053432	0.0066371
10	0.0054473	0.0047538	0.0059287
11	0.0055329	0.0048044	0.0060011
12	0.0055251	0.0047841	0.0060263
13	0.0052888	0.0045885	0.0057716
14	0.0057178	0.0050183	0.0062432
15	0.0061150	0.0053937	0.0066694
16	0.0064066	0.0055367	0.0069591
17	0.0063643	0.0056145	0.0069171
18	0.0055085	0.0047830	0.0060110
19	0.0059452	0.0051986	0.0064004
20	0.0060847	0.0053683	0.0065812
21	0.0060175	0.0054222	0.0065460
22	0.0066474	0.0060262	0.0071902
23	0.0013794	0.0013749	0.0015596

df_flips %>%
  group_by(chrom, SUPER) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>% 
  knitr::kable() 

`summarise()` has grouped output by 'chrom'. You can override using the
`.groups` argument.

chrom	SUPER	Beagle	Eagle	SHAPEIT
1	AFR	0.0048509	0.0038606	0.0052944
1	AMR	0.0055828	0.0049953	0.0061469
1	EAS	0.0074943	0.0068074	0.0080115
1	EUR	0.0054117	0.0049288	0.0057730
1	SAS	0.0070490	0.0062545	0.0077186
2	AFR	0.0049356	0.0039058	0.0054038
2	AMR	0.0058569	0.0051911	0.0063823
2	EAS	0.0076922	0.0070001	0.0083523
2	EUR	0.0053915	0.0048466	0.0058080
2	SAS	0.0072199	0.0063251	0.0078776
3	AFR	0.0046336	0.0036385	0.0050852
3	AMR	0.0054302	0.0048384	0.0059500
3	EAS	0.0072600	0.0065980	0.0077701
3	EUR	0.0052122	0.0047396	0.0055768
3	SAS	0.0067326	0.0059511	0.0073641
4	AFR	0.0043179	0.0034037	0.0047116
4	AMR	0.0052432	0.0047134	0.0057537
4	EAS	0.0066767	0.0061394	0.0072441
4	EUR	0.0048553	0.0043933	0.0052107
4	SAS	0.0064016	0.0056557	0.0069288
5	AFR	0.0046907	0.0036968	0.0051276
5	AMR	0.0053647	0.0048383	0.0059255
5	EAS	0.0071985	0.0065383	0.0078239
5	EUR	0.0051649	0.0046727	0.0055210
5	SAS	0.0068679	0.0060593	0.0074859
6	AFR	0.0042879	0.0034016	0.0046848
6	AMR	0.0049184	0.0044419	0.0053747
6	EAS	0.0065134	0.0059035	0.0069773
6	EUR	0.0045903	0.0041417	0.0048986
6	SAS	0.0061483	0.0054287	0.0066827
7	AFR	0.0047125	0.0038187	0.0052157
7	AMR	0.0054486	0.0048671	0.0059390
7	EAS	0.0072970	0.0066100	0.0078103
7	EUR	0.0050546	0.0046022	0.0054386
7	SAS	0.0068066	0.0060233	0.0074503
8	AFR	0.0046627	0.0036525	0.0051578
8	AMR	0.0055686	0.0050487	0.0061625
8	EAS	0.0074901	0.0067916	0.0079265
8	EUR	0.0051737	0.0046984	0.0055363
8	SAS	0.0067852	0.0060173	0.0074357
9	AFR	0.0053080	0.0042986	0.0058223
9	AMR	0.0058838	0.0052889	0.0064634
9	EAS	0.0079478	0.0072104	0.0084824
9	EUR	0.0057032	0.0051775	0.0060412
9	SAS	0.0073625	0.0065280	0.0080306
10	AFR	0.0047047	0.0037686	0.0051588
10	AMR	0.0053361	0.0047940	0.0058426
10	EAS	0.0069913	0.0063791	0.0075465
10	EUR	0.0050001	0.0045181	0.0053389
10	SAS	0.0066376	0.0059388	0.0072602
11	AFR	0.0046181	0.0036593	0.0050623
11	AMR	0.0055062	0.0049217	0.0059881
11	EAS	0.0071875	0.0065083	0.0077529
11	EUR	0.0050552	0.0045970	0.0054001
11	SAS	0.0069390	0.0061409	0.0075149
12	AFR	0.0046534	0.0036729	0.0051003
12	AMR	0.0054161	0.0048634	0.0059321
12	EAS	0.0071733	0.0065287	0.0077276
12	EUR	0.0050806	0.0045860	0.0054733
12	SAS	0.0069257	0.0060555	0.0076233
13	AFR	0.0045223	0.0035729	0.0049646
13	AMR	0.0051376	0.0045220	0.0056553
13	EAS	0.0068749	0.0062732	0.0073886
13	EUR	0.0049592	0.0044487	0.0052886
13	SAS	0.0064168	0.0058462	0.0071055
14	AFR	0.0048613	0.0039247	0.0053367
14	AMR	0.0058033	0.0051849	0.0063353
14	EAS	0.0072085	0.0066774	0.0078172
14	EUR	0.0052080	0.0047903	0.0056560
14	SAS	0.0069843	0.0062172	0.0076441
15	AFR	0.0052719	0.0043389	0.0057695
15	AMR	0.0058980	0.0052902	0.0064864
15	EAS	0.0078680	0.0071805	0.0084877
15	EUR	0.0057784	0.0052837	0.0061797
15	SAS	0.0073972	0.0066798	0.0081686
16	AFR	0.0054590	0.0044255	0.0059674
16	AMR	0.0062847	0.0055285	0.0068819
16	EAS	0.0083862	0.0075083	0.0089120
16	EUR	0.0058224	0.0053356	0.0063845
16	SAS	0.0079026	0.0067608	0.0084978
17	AFR	0.0053959	0.0044922	0.0059663
17	AMR	0.0061923	0.0055368	0.0067498
17	EAS	0.0084273	0.0076490	0.0089135
17	EUR	0.0058933	0.0053589	0.0063126
17	SAS	0.0077768	0.0069920	0.0085050
18	AFR	0.0045757	0.0036446	0.0050768
18	AMR	0.0055084	0.0048932	0.0060666
18	EAS	0.0072546	0.0065974	0.0077358
18	EUR	0.0051053	0.0046441	0.0054570
18	SAS	0.0067430	0.0059354	0.0073668
19	AFR	0.0050913	0.0041413	0.0055110
19	AMR	0.0058473	0.0052828	0.0063396
19	EAS	0.0077344	0.0069670	0.0082385
19	EUR	0.0055367	0.0050112	0.0058588
19	SAS	0.0071206	0.0063006	0.0077262
20	AFR	0.0050893	0.0041390	0.0055168
20	AMR	0.0060918	0.0054615	0.0066459
20	EAS	0.0080383	0.0074367	0.0086405
20	EUR	0.0055472	0.0051462	0.0059501
20	SAS	0.0074489	0.0066526	0.0080439
21	AFR	0.0053831	0.0045895	0.0059090
21	AMR	0.0059039	0.0054901	0.0064466
21	EAS	0.0073858	0.0067774	0.0078760
21	EUR	0.0055923	0.0051591	0.0060380
21	SAS	0.0070768	0.0064655	0.0077258
22	AFR	0.0059118	0.0050632	0.0064401
22	AMR	0.0065342	0.0060244	0.0070762
22	EAS	0.0082989	0.0077582	0.0088412
22	EUR	0.0060571	0.0056668	0.0064708
22	SAS	0.0079135	0.0072917	0.0086547
23	AFR	0.0010081	0.0009991	0.0011945
23	AMR	0.0011009	0.0010802	0.0012704
23	EAS	0.0019555	0.0019427	0.0021114
23	EUR	0.0012423	0.0012304	0.0014230
23	SAS	0.0015903	0.0016220	0.0017988

df_flips %>%
  group_by(chrom) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>%
  pivot_longer(Beagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  ggplot(aes(x = chrom, y = error_rate, colour = method, shape = method)) +
  geom_point(size=3) +
  theme_bw() +
  xlab("Chromosome") +
  ylab("Flip Rate") +
  labs(colour = "Method", shape = "Method") +
  scale_colour_brewer(palette = "Set2") +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5)) +
  scale_x_continuous("Chromosome", labels = as.character(unique(df_flips$chrom)), breaks = unique(df_flips$chrom))

Past versions of unnamed-chunk-22-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
17d41d5	Andy Beck	2024-05-22
d7d8f5a	Andy Beck	2024-05-22
da672c2	Andy Beck	2024-05-22

df_flips %>%
  group_by(chrom, SUPER) %>%
  summarise(Beagle = mean(Beagle),
            Eagle = mean(Eagle),
            SHAPEIT = mean(SHAPEIT)) %>%
  pivot_longer(Beagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  ggplot(aes(x = chrom, y = error_rate, colour = SUPER, shape = method)) +
  geom_point(size=2) +
  theme_bw() +
  ylab("Flip Rate") +
  xlab("Chromosome") +
  labs(colour = "Population", shape = "Method") +
  scale_colour_brewer(palette = "Set1") +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5)) +
  scale_x_continuous("Chromosome", labels = as.character(unique(df_flips$chrom)), breaks = unique(df_flips$chrom))

`summarise()` has grouped output by 'chrom'. You can override using the
`.groups` argument.

Past versions of unnamed-chunk-22-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
17d41d5	Andy Beck	2024-05-22
d7d8f5a	Andy Beck	2024-05-22
da672c2	Andy Beck	2024-05-22

# Beagle
autosomes <- df_flips %>% filter(chrom < 23) %>% pull(Beagle)
chrX <- df_flips %>% filter(chrom == 23) %>% pull(Beagle)
t.test(autosomes, chrX) %>% broom::tidy()

# A tibble: 1 × 10
  estimate estimate1 estimate2 statistic p.value parameter conf.low conf.high
     <dbl>     <dbl>     <dbl>     <dbl>   <dbl>     <dbl>    <dbl>     <dbl>
1  0.00438   0.00576   0.00138      207.       0     2957.  0.00434   0.00442
# ℹ 2 more variables: method <chr>, alternative <chr>

# Eagle
autosomes <- df_flips %>% filter(chrom < 23) %>% pull(Eagle)
chrX <- df_flips %>% filter(chrom == 23) %>% pull(Eagle)
t.test(autosomes, chrX) %>% broom::tidy()

# A tibble: 1 × 10
  estimate estimate1 estimate2 statistic p.value parameter conf.low conf.high
     <dbl>     <dbl>     <dbl>     <dbl>   <dbl>     <dbl>    <dbl>     <dbl>
1  0.00367   0.00504   0.00137      176.       0     3336.  0.00362   0.00371
# ℹ 2 more variables: method <chr>, alternative <chr>

# SHAPEIT
autosomes <- df_flips %>% filter(chrom < 23) %>% pull(SHAPEIT)
chrX <- df_flips %>% filter(chrom == 23) %>% pull(SHAPEIT)
t.test(autosomes, chrX) %>% broom::tidy()

# A tibble: 1 × 10
  estimate estimate1 estimate2 statistic p.value parameter conf.low conf.high
     <dbl>     <dbl>     <dbl>     <dbl>   <dbl>     <dbl>    <dbl>     <dbl>
1  0.00470   0.00626   0.00156      217.       0     2802.  0.00466   0.00475
# ℹ 2 more variables: method <chr>, alternative <chr>

mod_fit <- df_flips %>%
  filter(chrom == 1) %>%
  pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  {lmerTest::lmer(error_rate ~ method + (1|pair_id), data = .)}

df_anova <- anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = 1)

df_pairwise <- emmeans::emmeans(mod_fit, ~ method) %>% pairs() %>% broom::tidy() %>% mutate(chrom=1)

for(i in 2:23){
  mod_fit <- df_flips %>%
    filter(chrom == i) %>%
    pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
    {lmerTest::lmer(error_rate ~ method + (1|pair_id), data = .)}
  
  df_anova <- df_anova %>% bind_rows({anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = i)})
  df_pairwise <- df_pairwise %>% bind_rows({
    emmeans::emmeans(mod_fit, ~ method) %>% pairs() %>% broom::tidy() %>% mutate(chrom=i)})
}

df_anova %>%
  knitr::kable()

term	sumsq	meansq	NumDF	DenDF	statistic	p.value	chrom
method	0.0004701	0.0002351	2	1202	3013.4749	0	1
method	0.0005348	0.0002674	2	1202	3318.1790	0	2
method	0.0004579	0.0002290	2	1202	3011.9306	0	3
method	0.0003898	0.0001949	2	1202	2569.4671	0	4
method	0.0004617	0.0002308	2	1202	2718.1027	0	5
method	0.0003572	0.0001786	2	1202	2679.0043	0	6
method	0.0004406	0.0002203	2	1202	2572.5825	0	7
method	0.0004686	0.0002343	2	1202	2046.3998	0	8
method	0.0005101	0.0002551	2	1202	2506.4370	0	9
method	0.0004200	0.0002100	2	1202	2375.3062	0	10
method	0.0004379	0.0002189	2	1202	2188.9479	0	11
method	0.0004703	0.0002351	2	1202	2259.7295	0	12
method	0.0004261	0.0002130	2	1202	1679.8712	0	13
method	0.0004547	0.0002273	2	1202	1921.3314	0	14
method	0.0004926	0.0002463	2	1202	1943.4193	0	15
method	0.0006191	0.0003095	2	1202	1781.7578	0	16
method	0.0005146	0.0002573	2	1202	1661.9270	0	17
method	0.0004589	0.0002294	2	1202	1880.3071	0	18
method	0.0004433	0.0002216	2	1202	1421.4820	0	19
method	0.0004476	0.0002238	2	1202	1429.7051	0	20
method	0.0003806	0.0001903	2	1202	991.8020	0	21
method	0.0004084	0.0002042	2	1202	887.5711	0	22
method	0.0000222	0.0000111	2	1998	638.9949	0	23

df_pairwise %>%
  knitr::kable()

term	contrast	null.value	estimate	std.error	df	statistic	adj.p.value	chrom
method	Beagle - Eagle	0	0.0007445	1.61e-05	1202	46.2469554	0.0000000	1
method	Beagle - SHAPEIT	0	-0.0004971	1.61e-05	1202	-30.8776948	0.0000000	1
method	Eagle - SHAPEIT	0	-0.0012416	1.61e-05	1202	-77.1246502	0.0000000	1
method	Beagle - Eagle	0	0.0008013	1.64e-05	1202	48.9749823	0.0000000	2
method	Beagle - SHAPEIT	0	-0.0005218	1.64e-05	1202	-31.8894262	0.0000000	2
method	Eagle - SHAPEIT	0	-0.0013231	1.64e-05	1202	-80.8644085	0.0000000	2
method	Beagle - Eagle	0	0.0007405	1.59e-05	1202	46.5936902	0.0000000	3
method	Beagle - SHAPEIT	0	-0.0004840	1.59e-05	1202	-30.4587775	0.0000000	3
method	Eagle - SHAPEIT	0	-0.0012245	1.59e-05	1202	-77.0524677	0.0000000	3
method	Beagle - Eagle	0	0.0006775	1.59e-05	1202	42.6785421	0.0000000	4
method	Beagle - SHAPEIT	0	-0.0004531	1.59e-05	1202	-28.5416595	0.0000000	4
method	Eagle - SHAPEIT	0	-0.0011306	1.59e-05	1202	-71.2202016	0.0000000	4
method	Beagle - Eagle	0	0.0007323	1.68e-05	1202	43.5946151	0.0000000	5
method	Beagle - SHAPEIT	0	-0.0004988	1.68e-05	1202	-29.6981900	0.0000000	5
method	Eagle - SHAPEIT	0	-0.0012311	1.68e-05	1202	-73.2928051	0.0000000	5
method	Beagle - Eagle	0	0.0006586	1.49e-05	1202	44.2577383	0.0000000	6
method	Beagle - SHAPEIT	0	-0.0004221	1.49e-05	1202	-28.3631688	0.0000000	6
method	Eagle - SHAPEIT	0	-0.0010807	1.49e-05	1202	-72.6209071	0.0000000	6
method	Beagle - Eagle	0	0.0007039	1.69e-05	1202	41.7366488	0.0000000	7
method	Beagle - SHAPEIT	0	-0.0005001	1.69e-05	1202	-29.6530856	0.0000000	7
method	Eagle - SHAPEIT	0	-0.0012041	1.69e-05	1202	-71.3897344	0.0000000	7
method	Beagle - Eagle	0	0.0007321	1.95e-05	1202	37.5369195	0.0000000	8
method	Beagle - SHAPEIT	0	-0.0005089	1.95e-05	1202	-26.0961643	0.0000000	8
method	Eagle - SHAPEIT	0	-0.0012410	1.95e-05	1202	-63.6330838	0.0000000	8
method	Beagle - Eagle	0	0.0007718	1.84e-05	1202	41.9768441	0.0000000	9
method	Beagle - SHAPEIT	0	-0.0005220	1.84e-05	1202	-28.3888396	0.0000000	9
method	Eagle - SHAPEIT	0	-0.0012938	1.84e-05	1202	-70.3656836	0.0000000	9
method	Beagle - Eagle	0	0.0006935	1.71e-05	1202	40.4636630	0.0000000	10
method	Beagle - SHAPEIT	0	-0.0004814	1.71e-05	1202	-28.0897810	0.0000000	10
method	Eagle - SHAPEIT	0	-0.0011749	1.71e-05	1202	-68.5534440	0.0000000	10
method	Beagle - Eagle	0	0.0007285	1.82e-05	1202	39.9658214	0.0000000	11
method	Beagle - SHAPEIT	0	-0.0004682	1.82e-05	1202	-25.6840547	0.0000000	11
method	Eagle - SHAPEIT	0	-0.0011967	1.82e-05	1202	-65.6498761	0.0000000	11
method	Beagle - Eagle	0	0.0007410	1.86e-05	1202	39.8553280	0.0000000	12
method	Beagle - SHAPEIT	0	-0.0005012	1.86e-05	1202	-26.9579298	0.0000000	12
method	Eagle - SHAPEIT	0	-0.0012422	1.86e-05	1202	-66.8132578	0.0000000	12
method	Beagle - Eagle	0	0.0007003	2.05e-05	1202	34.1204928	0.0000000	13
method	Beagle - SHAPEIT	0	-0.0004827	2.05e-05	1202	-23.5186982	0.0000000	13
method	Eagle - SHAPEIT	0	-0.0011831	2.05e-05	1202	-57.6391910	0.0000000	13
method	Beagle - Eagle	0	0.0006995	1.98e-05	1202	35.2821507	0.0000000	14
method	Beagle - SHAPEIT	0	-0.0005254	1.98e-05	1202	-26.4993205	0.0000000	14
method	Eagle - SHAPEIT	0	-0.0012249	1.98e-05	1202	-61.7814712	0.0000000	14
method	Beagle - Eagle	0	0.0007213	2.05e-05	1202	35.1503531	0.0000000	15
method	Beagle - SHAPEIT	0	-0.0005544	2.05e-05	1202	-27.0170709	0.0000000	15
method	Eagle - SHAPEIT	0	-0.0012757	2.05e-05	1202	-62.1674240	0.0000000	15
method	Beagle - Eagle	0	0.0008699	2.40e-05	1202	36.2100322	0.0000000	16
method	Beagle - SHAPEIT	0	-0.0005525	2.40e-05	1202	-22.9956142	0.0000000	16
method	Eagle - SHAPEIT	0	-0.0014224	2.40e-05	1202	-59.2056464	0.0000000	16
method	Beagle - Eagle	0	0.0007498	2.27e-05	1202	33.0596397	0.0000000	17
method	Beagle - SHAPEIT	0	-0.0005528	2.27e-05	1202	-24.3747719	0.0000000	17
method	Eagle - SHAPEIT	0	-0.0013026	2.27e-05	1202	-57.4344116	0.0000000	17
method	Beagle - Eagle	0	0.0007255	2.01e-05	1202	36.0323784	0.0000000	18
method	Beagle - SHAPEIT	0	-0.0005025	2.01e-05	1202	-24.9571910	0.0000000	18
method	Eagle - SHAPEIT	0	-0.0012280	2.01e-05	1202	-60.9895694	0.0000000	18
method	Beagle - Eagle	0	0.0007466	2.28e-05	1202	32.8036707	0.0000000	19
method	Beagle - SHAPEIT	0	-0.0004552	2.28e-05	1202	-20.0009441	0.0000000	19
method	Eagle - SHAPEIT	0	-0.0012018	2.28e-05	1202	-52.8046148	0.0000000	19
method	Beagle - Eagle	0	0.0007164	2.28e-05	1202	31.4130234	0.0000000	20
method	Beagle - SHAPEIT	0	-0.0004965	2.28e-05	1202	-21.7698034	0.0000000	20
method	Eagle - SHAPEIT	0	-0.0012129	2.28e-05	1202	-53.1828268	0.0000000	20
method	Beagle - Eagle	0	0.0005952	2.52e-05	1202	23.5757485	0.0000000	21
method	Beagle - SHAPEIT	0	-0.0005286	2.52e-05	1202	-20.9358326	0.0000000	21
method	Eagle - SHAPEIT	0	-0.0011238	2.52e-05	1202	-44.5115811	0.0000000	21
method	Beagle - Eagle	0	0.0006212	2.76e-05	1202	22.4682068	0.0000000	22
method	Beagle - SHAPEIT	0	-0.0005428	2.76e-05	1202	-19.6324060	0.0000000	22
method	Eagle - SHAPEIT	0	-0.0011640	2.76e-05	1202	-42.1006129	0.0000000	22
method	Beagle - Eagle	0	0.0000045	5.90e-06	1998	0.7705121	0.7211872	23
method	Beagle - SHAPEIT	0	-0.0001802	5.90e-06	1998	-30.5670808	0.0000000	23
method	Eagle - SHAPEIT	0	-0.0001848	5.90e-06	1998	-31.3375929	0.0000000	23

mod_fit <- df_flips %>%
  filter(chrom == 1) %>%
  pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
  {lmerTest::lmer(error_rate ~ method*SUPER + (1|pair_id), data = .)}

df_pop_anova <- anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = 1)

df_pop_pairwise <- emmeans::emmeans(mod_fit, ~ method | SUPER) %>% pairs() %>% broom::tidy() %>% mutate(chrom=1)
df_pop_pop <- emmeans::emmeans(mod_fit, ~ SUPER | method) %>% pairs() %>% broom::tidy() %>% mutate(chrom = 1)

for(i in 2:23){
  mod_fit <- df_flips %>%
    filter(chrom == i) %>%
    pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
    {lmerTest::lmer(error_rate ~ method*SUPER + (1|pair_id), data = .)}
  
  df_pop_anova <- df_pop_anova %>% bind_rows({anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = i)})
  df_pop_pairwise <- df_pop_pairwise %>% bind_rows({
    emmeans::emmeans(mod_fit, ~ method | SUPER) %>% pairs() %>% broom::tidy() %>% mutate(chrom=i)})
  df_pop_pop <- df_pop_pop %>% bind_rows({
    emmeans::emmeans(mod_fit, ~ SUPER | method) %>% pairs() %>% broom::tidy() %>% mutate(chrom = i)})
}

df_pop_anova %>%
  knitr::kable()

term	sumsq	meansq	NumDF	DenDF	statistic	p.value	chrom
method	0.0003967	0.0001983	2	1194.0000	3192.826276	0.0000000	1
SUPER	0.0000276	0.0000069	4	597.0000	111.269503	0.0000000	1
method:SUPER	0.0000196	0.0000024	8	1194.0000	39.413286	0.0000000	1
method	0.0004588	0.0002294	2	1194.0000	3464.684510	0.0000000	2
SUPER	0.0000327	0.0000082	4	597.0000	123.522649	0.0000000	2
method:SUPER	0.0000178	0.0000022	8	1194.0000	33.617845	0.0000000	2
method	0.0003820	0.0001910	2	1194.0000	3181.378464	0.0000000	3
SUPER	0.0000271	0.0000068	4	597.0000	112.819852	0.0000000	3
method:SUPER	0.0000197	0.0000025	8	1194.0000	40.986641	0.0000000	3
method	0.0003275	0.0001637	2	1194.0000	2558.720305	0.0000000	4
SUPER	0.0000312	0.0000078	4	597.0000	121.768081	0.0000000	4
method:SUPER	0.0000148	0.0000018	8	1194.0000	28.856281	0.0000000	4
method	0.0003935	0.0001968	2	1194.0000	2891.005556	0.0000000	5
SUPER	0.0000287	0.0000072	4	597.0000	105.490039	0.0000000	5
method:SUPER	0.0000208	0.0000026	8	1194.0000	38.224530	0.0000000	5
method	0.0003006	0.0001503	2	1194.0000	2799.000055	0.0000000	6
SUPER	0.0000219	0.0000055	4	597.0000	101.834616	0.0000000	6
method:SUPER	0.0000160	0.0000020	8	1194.0000	37.296767	0.0000000	6
method	0.0003749	0.0001874	2	1194.0000	2578.764416	0.0000000	7
SUPER	0.0000327	0.0000082	4	597.0000	112.299606	0.0000000	7
method:SUPER	0.0000161	0.0000020	8	1194.0000	27.745892	0.0000000	7
method	0.0003851	0.0001926	2	1194.0000	2020.831393	0.0000000	8
SUPER	0.0000425	0.0000106	4	597.0000	111.515524	0.0000000	8
method:SUPER	0.0000238	0.0000030	8	1194.0000	31.262187	0.0000000	8
method	0.0004287	0.0002143	2	1194.0000	2538.806313	0.0000000	9
SUPER	0.0000345	0.0000086	4	597.0000	102.026700	0.0000000	9
method:SUPER	0.0000215	0.0000027	8	1194.0000	31.857680	0.0000000	9
method	0.0003517	0.0001759	2	1194.0000	2356.376792	0.0000000	10
SUPER	0.0000328	0.0000082	4	596.9999	109.877832	0.0000000	10
method:SUPER	0.0000172	0.0000021	8	1194.0000	28.739506	0.0000000	10
method	0.0003711	0.0001855	2	1194.0000	2178.697681	0.0000000	11
SUPER	0.0000366	0.0000091	4	597.0000	107.358104	0.0000000	11
method:SUPER	0.0000185	0.0000023	8	1194.0000	27.220855	0.0000000	11
method	0.0004031	0.0002016	2	1194.0000	2319.701014	0.0000000	12
SUPER	0.0000358	0.0000090	4	596.9999	103.017010	0.0000000	12
method:SUPER	0.0000213	0.0000027	8	1194.0000	30.677480	0.0000000	12
method	0.0003504	0.0001752	2	1194.0000	1535.886331	0.0000000	13
SUPER	0.0000432	0.0000108	4	597.0000	94.754693	0.0000000	13
method:SUPER	0.0000162	0.0000020	8	1194.0000	17.764775	0.0000000	13
method	0.0003811	0.0001906	2	1194.0000	1821.579291	0.0000000	14
SUPER	0.0000400	0.0000100	4	597.0000	95.492420	0.0000000	14
method:SUPER	0.0000173	0.0000022	8	1194.0000	20.672648	0.0000000	14
method	0.0004234	0.0002117	2	1194.0000	1858.557476	0.0000000	15
SUPER	0.0000414	0.0000104	4	597.0000	90.917098	0.0000000	15
method:SUPER	0.0000163	0.0000020	8	1194.0000	17.932999	0.0000000	15
method	0.0005389	0.0002695	2	1194.0000	1694.618761	0.0000000	16
SUPER	0.0000573	0.0000143	4	597.0000	90.099898	0.0000000	16
method:SUPER	0.0000190	0.0000024	8	1194.0000	14.913350	0.0000000	16
method	0.0004385	0.0002193	2	1194.0000	1515.063291	0.0000000	17
SUPER	0.0000544	0.0000136	4	597.0000	93.955710	0.0000000	17
method:SUPER	0.0000133	0.0000017	8	1194.0000	11.491384	0.0000000	17
method	0.0003825	0.0001913	2	1194.0000	1774.755328	0.0000000	18
SUPER	0.0000479	0.0000120	4	597.0000	111.168244	0.0000000	18
method:SUPER	0.0000180	0.0000023	8	1194.0000	20.880766	0.0000000	18
method	0.0003829	0.0001915	2	1194.0000	1337.730530	0.0000000	19
SUPER	0.0000500	0.0000125	4	597.0000	87.270523	0.0000000	19
method:SUPER	0.0000165	0.0000021	8	1194.0000	14.436580	0.0000000	19
method	0.0003781	0.0001890	2	1194.0000	1327.232824	0.0000000	20
SUPER	0.0000550	0.0000137	4	597.0000	96.500071	0.0000000	20
method:SUPER	0.0000181	0.0000023	8	1194.0000	15.887647	0.0000000	20
method	0.0003217	0.0001609	2	1194.0000	879.761890	0.0000000	21
SUPER	0.0000411	0.0000103	4	597.0000	56.153871	0.0000000	21
method:SUPER	0.0000123	0.0000015	8	1194.0000	8.418774	0.0000000	21
method	0.0003411	0.0001706	2	1194.0000	785.671346	0.0000000	22
SUPER	0.0000543	0.0000136	4	597.0000	62.530883	0.0000000	22
method:SUPER	0.0000173	0.0000022	8	1194.0000	9.977930	0.0000000	22
method	0.0000222	0.0000111	2	1990.0000	641.105027	0.0000000	23
SUPER	0.0000178	0.0000044	4	995.0000	256.572985	0.0000000	23
method:SUPER	0.0000003	0.0000000	8	1990.0000	1.824723	0.0681454	23

df_pop_pairwise %>% knitr::kable()

SUPER	term	contrast	null.value	estimate	std.error	df	statistic	adj.p.value	chrom
AFR	method	Beagle - Eagle	0	0.0009903	2.49e-05	1194	39.8313731	0.0000000	1
AFR	method	Beagle - SHAPEIT	0	-0.0004435	2.49e-05	1194	-17.8370961	0.0000000	1
AFR	method	Eagle - SHAPEIT	0	-0.0014338	2.49e-05	1194	-57.6684692	0.0000000	1
AMR	method	Beagle - Eagle	0	0.0005874	3.01e-05	1194	19.5069897	0.0000000	1
AMR	method	Beagle - SHAPEIT	0	-0.0005642	3.01e-05	1194	-18.7336247	0.0000000	1
AMR	method	Eagle - SHAPEIT	0	-0.0011516	3.01e-05	1194	-38.2406145	0.0000000	1
EAS	method	Beagle - Eagle	0	0.0006869	4.15e-05	1194	16.5360004	0.0000000	1
EAS	method	Beagle - SHAPEIT	0	-0.0005172	4.15e-05	1194	-12.4506624	0.0000000	1
EAS	method	Eagle - SHAPEIT	0	-0.0012041	4.15e-05	1194	-28.9866628	0.0000000	1
EUR	method	Beagle - Eagle	0	0.0004829	3.41e-05	1194	14.1700951	0.0000000	1
EUR	method	Beagle - SHAPEIT	0	-0.0003613	3.41e-05	1194	-10.6031851	0.0000000	1
EUR	method	Eagle - SHAPEIT	0	-0.0008442	3.41e-05	1194	-24.7732801	0.0000000	1
SAS	method	Beagle - Eagle	0	0.0007945	3.82e-05	1194	20.7802550	0.0000000	1
SAS	method	Beagle - SHAPEIT	0	-0.0006696	3.82e-05	1194	-17.5129608	0.0000000	1
SAS	method	Eagle - SHAPEIT	0	-0.0014640	3.82e-05	1194	-38.2932157	0.0000000	1
AFR	method	Beagle - Eagle	0	0.0010298	2.57e-05	1194	40.1220106	0.0000000	2
AFR	method	Beagle - SHAPEIT	0	-0.0004682	2.57e-05	1194	-18.2433930	0.0000000	2
AFR	method	Eagle - SHAPEIT	0	-0.0014980	2.57e-05	1194	-58.3654037	0.0000000	2
AMR	method	Beagle - Eagle	0	0.0006658	3.11e-05	1194	21.4151192	0.0000000	2
AMR	method	Beagle - SHAPEIT	0	-0.0005254	3.11e-05	1194	-16.9002652	0.0000000	2
AMR	method	Eagle - SHAPEIT	0	-0.0011912	3.11e-05	1194	-38.3153843	0.0000000	2
EAS	method	Beagle - Eagle	0	0.0006921	4.29e-05	1194	16.1382729	0.0000000	2
EAS	method	Beagle - SHAPEIT	0	-0.0006601	4.29e-05	1194	-15.3916948	0.0000000	2
EAS	method	Eagle - SHAPEIT	0	-0.0013521	4.29e-05	1194	-31.5299677	0.0000000	2
EUR	method	Beagle - Eagle	0	0.0005449	3.52e-05	1194	15.4903048	0.0000000	2
EUR	method	Beagle - SHAPEIT	0	-0.0004166	3.52e-05	1194	-11.8414627	0.0000000	2
EUR	method	Eagle - SHAPEIT	0	-0.0009615	3.52e-05	1194	-27.3317674	0.0000000	2
SAS	method	Beagle - Eagle	0	0.0008948	3.95e-05	1194	22.6702712	0.0000000	2
SAS	method	Beagle - SHAPEIT	0	-0.0006577	3.95e-05	1194	-16.6646840	0.0000000	2
SAS	method	Eagle - SHAPEIT	0	-0.0015525	3.95e-05	1194	-39.3349552	0.0000000	2
AFR	method	Beagle - Eagle	0	0.0009951	2.44e-05	1194	40.7119464	0.0000000	3
AFR	method	Beagle - SHAPEIT	0	-0.0004516	2.44e-05	1194	-18.4748575	0.0000000	3
AFR	method	Eagle - SHAPEIT	0	-0.0014466	2.44e-05	1194	-59.1868040	0.0000000	3
AMR	method	Beagle - Eagle	0	0.0005918	2.96e-05	1194	19.9906523	0.0000000	3
AMR	method	Beagle - SHAPEIT	0	-0.0005198	2.96e-05	1194	-17.5587685	0.0000000	3
AMR	method	Eagle - SHAPEIT	0	-0.0011117	2.96e-05	1194	-37.5494207	0.0000000	3
EAS	method	Beagle - Eagle	0	0.0006620	4.08e-05	1194	16.2104761	0.0000000	3
EAS	method	Beagle - SHAPEIT	0	-0.0005101	4.08e-05	1194	-12.4908586	0.0000000	3
EAS	method	Eagle - SHAPEIT	0	-0.0011721	4.08e-05	1194	-28.7013347	0.0000000	3
EUR	method	Beagle - Eagle	0	0.0004726	3.35e-05	1194	14.1075643	0.0000000	3
EUR	method	Beagle - SHAPEIT	0	-0.0003646	3.35e-05	1194	-10.8842658	0.0000000	3
EUR	method	Eagle - SHAPEIT	0	-0.0008372	3.35e-05	1194	-24.9918301	0.0000000	3
SAS	method	Beagle - Eagle	0	0.0007816	3.76e-05	1194	20.7940464	0.0000000	3
SAS	method	Beagle - SHAPEIT	0	-0.0006314	3.76e-05	1194	-16.8001160	0.0000000	3
SAS	method	Eagle - SHAPEIT	0	-0.0014130	3.76e-05	1194	-37.5941624	0.0000000	3
AFR	method	Beagle - Eagle	0	0.0009142	2.52e-05	1194	36.2285157	0.0000000	4
AFR	method	Beagle - SHAPEIT	0	-0.0003938	2.52e-05	1194	-15.6048424	0.0000000	4
AFR	method	Eagle - SHAPEIT	0	-0.0013079	2.52e-05	1194	-51.8333581	0.0000000	4
AMR	method	Beagle - Eagle	0	0.0005299	3.06e-05	1194	17.3368943	0.0000000	4
AMR	method	Beagle - SHAPEIT	0	-0.0005104	3.06e-05	1194	-16.6995945	0.0000000	4
AMR	method	Eagle - SHAPEIT	0	-0.0010403	3.06e-05	1194	-34.0364888	0.0000000	4
EAS	method	Beagle - Eagle	0	0.0005373	4.22e-05	1194	12.7438226	0.0000000	4
EAS	method	Beagle - SHAPEIT	0	-0.0005674	4.22e-05	1194	-13.4574360	0.0000000	4
EAS	method	Eagle - SHAPEIT	0	-0.0011047	4.22e-05	1194	-26.2012585	0.0000000	4
EUR	method	Beagle - Eagle	0	0.0004620	3.46e-05	1194	13.3594147	0.0000000	4
EUR	method	Beagle - SHAPEIT	0	-0.0003554	3.46e-05	1194	-10.2758253	0.0000000	4
EUR	method	Eagle - SHAPEIT	0	-0.0008174	3.46e-05	1194	-23.6352400	0.0000000	4
SAS	method	Beagle - Eagle	0	0.0007459	3.88e-05	1194	19.2217748	0.0000000	4
SAS	method	Beagle - SHAPEIT	0	-0.0005272	3.88e-05	1194	-13.5866435	0.0000000	4
SAS	method	Eagle - SHAPEIT	0	-0.0012731	3.88e-05	1194	-32.8084183	0.0000000	4
AFR	method	Beagle - Eagle	0	0.0009939	2.60e-05	1194	38.1919929	0.0000000	5
AFR	method	Beagle - SHAPEIT	0	-0.0004369	2.60e-05	1194	-16.7895457	0.0000000	5
AFR	method	Eagle - SHAPEIT	0	-0.0014308	2.60e-05	1194	-54.9815386	0.0000000	5
AMR	method	Beagle - Eagle	0	0.0005264	3.15e-05	1194	16.6998560	0.0000000	5
AMR	method	Beagle - SHAPEIT	0	-0.0005608	3.15e-05	1194	-17.7900173	0.0000000	5
AMR	method	Eagle - SHAPEIT	0	-0.0010872	3.15e-05	1194	-34.4898733	0.0000000	5
EAS	method	Beagle - Eagle	0	0.0006602	4.35e-05	1194	15.1833345	0.0000000	5
EAS	method	Beagle - SHAPEIT	0	-0.0006254	4.35e-05	1194	-14.3823834	0.0000000	5
EAS	method	Eagle - SHAPEIT	0	-0.0012856	4.35e-05	1194	-29.5657179	0.0000000	5
EUR	method	Beagle - Eagle	0	0.0004922	3.57e-05	1194	13.8001126	0.0000000	5
EUR	method	Beagle - SHAPEIT	0	-0.0003560	3.57e-05	1194	-9.9820022	0.0000000	5
EUR	method	Eagle - SHAPEIT	0	-0.0008483	3.57e-05	1194	-23.7821148	0.0000000	5
SAS	method	Beagle - Eagle	0	0.0008086	4.00e-05	1194	20.2052594	0.0000000	5
SAS	method	Beagle - SHAPEIT	0	-0.0006180	4.00e-05	1194	-15.4439938	0.0000000	5
SAS	method	Eagle - SHAPEIT	0	-0.0014266	4.00e-05	1194	-35.6492532	0.0000000	5
AFR	method	Beagle - Eagle	0	0.0008863	2.31e-05	1194	38.3462428	0.0000000	6
AFR	method	Beagle - SHAPEIT	0	-0.0003968	2.31e-05	1194	-17.1692991	0.0000000	6
AFR	method	Eagle - SHAPEIT	0	-0.0012832	2.31e-05	1194	-55.5155419	0.0000000	6
AMR	method	Beagle - Eagle	0	0.0004764	2.80e-05	1194	17.0174981	0.0000000	6
AMR	method	Beagle - SHAPEIT	0	-0.0004563	2.80e-05	1194	-16.2991758	0.0000000	6
AMR	method	Eagle - SHAPEIT	0	-0.0009328	2.80e-05	1194	-33.3166740	0.0000000	6
EAS	method	Beagle - Eagle	0	0.0006098	3.86e-05	1194	15.7914101	0.0000000	6
EAS	method	Beagle - SHAPEIT	0	-0.0004639	3.86e-05	1194	-12.0122281	0.0000000	6
EAS	method	Eagle - SHAPEIT	0	-0.0010737	3.86e-05	1194	-27.8036382	0.0000000	6
EUR	method	Beagle - Eagle	0	0.0004486	3.17e-05	1194	14.1608269	0.0000000	6
EUR	method	Beagle - SHAPEIT	0	-0.0003083	3.17e-05	1194	-9.7326504	0.0000000	6
EUR	method	Eagle - SHAPEIT	0	-0.0007569	3.17e-05	1194	-23.8934773	0.0000000	6
SAS	method	Beagle - Eagle	0	0.0007196	3.55e-05	1194	20.2457655	0.0000000	6
SAS	method	Beagle - SHAPEIT	0	-0.0005344	3.55e-05	1194	-15.0363649	0.0000000	6
SAS	method	Eagle - SHAPEIT	0	-0.0012540	3.55e-05	1194	-35.2821303	0.0000000	6
AFR	method	Beagle - Eagle	0	0.0008938	2.69e-05	1194	33.2346534	0.0000000	7
AFR	method	Beagle - SHAPEIT	0	-0.0005032	2.69e-05	1194	-18.7094220	0.0000000	7
AFR	method	Eagle - SHAPEIT	0	-0.0013969	2.69e-05	1194	-51.9440755	0.0000000	7
AMR	method	Beagle - Eagle	0	0.0005815	3.26e-05	1194	17.8518350	0.0000000	7
AMR	method	Beagle - SHAPEIT	0	-0.0004904	3.26e-05	1194	-15.0550500	0.0000000	7
AMR	method	Eagle - SHAPEIT	0	-0.0010719	3.26e-05	1194	-32.9068849	0.0000000	7
EAS	method	Beagle - Eagle	0	0.0006870	4.49e-05	1194	15.2899737	0.0000000	7
EAS	method	Beagle - SHAPEIT	0	-0.0005133	4.49e-05	1194	-11.4239565	0.0000000	7
EAS	method	Eagle - SHAPEIT	0	-0.0012004	4.49e-05	1194	-26.7139302	0.0000000	7
EUR	method	Beagle - Eagle	0	0.0004524	3.69e-05	1194	12.2724546	0.0000000	7
EUR	method	Beagle - SHAPEIT	0	-0.0003840	3.69e-05	1194	-10.4192855	0.0000000	7
EUR	method	Eagle - SHAPEIT	0	-0.0008364	3.69e-05	1194	-22.6917401	0.0000000	7
SAS	method	Beagle - Eagle	0	0.0007833	4.14e-05	1194	18.9413622	0.0000000	7
SAS	method	Beagle - SHAPEIT	0	-0.0006436	4.14e-05	1194	-15.5630446	0.0000000	7
SAS	method	Eagle - SHAPEIT	0	-0.0014269	4.14e-05	1194	-34.5044068	0.0000000	7
AFR	method	Beagle - Eagle	0	0.0010102	3.08e-05	1194	32.8076986	0.0000000	8
AFR	method	Beagle - SHAPEIT	0	-0.0004951	3.08e-05	1194	-16.0769328	0.0000000	8
AFR	method	Eagle - SHAPEIT	0	-0.0015053	3.08e-05	1194	-48.8846314	0.0000000	8
AMR	method	Beagle - Eagle	0	0.0005199	3.73e-05	1194	13.9391027	0.0000000	8
AMR	method	Beagle - SHAPEIT	0	-0.0005939	3.73e-05	1194	-15.9235135	0.0000000	8
AMR	method	Eagle - SHAPEIT	0	-0.0011138	3.73e-05	1194	-29.8626162	0.0000000	8
EAS	method	Beagle - Eagle	0	0.0006985	5.14e-05	1194	13.5757631	0.0000000	8
EAS	method	Beagle - SHAPEIT	0	-0.0004364	5.14e-05	1194	-8.4815494	0.0000000	8
EAS	method	Eagle - SHAPEIT	0	-0.0011348	5.14e-05	1194	-22.0573125	0.0000000	8
EUR	method	Beagle - Eagle	0	0.0004753	4.22e-05	1194	11.2625084	0.0000000	8
EUR	method	Beagle - SHAPEIT	0	-0.0003626	4.22e-05	1194	-8.5912484	0.0000000	8
EUR	method	Eagle - SHAPEIT	0	-0.0008379	4.22e-05	1194	-19.8537569	0.0000000	8
SAS	method	Beagle - Eagle	0	0.0007679	4.74e-05	1194	16.2171959	0.0000000	8
SAS	method	Beagle - SHAPEIT	0	-0.0006506	4.74e-05	1194	-13.7388077	0.0000000	8
SAS	method	Eagle - SHAPEIT	0	-0.0014185	4.74e-05	1194	-29.9560036	0.0000000	8
AFR	method	Beagle - Eagle	0	0.0010093	2.90e-05	1194	34.8231128	0.0000000	9
AFR	method	Beagle - SHAPEIT	0	-0.0005144	2.90e-05	1194	-17.7462965	0.0000000	9
AFR	method	Eagle - SHAPEIT	0	-0.0015237	2.90e-05	1194	-52.5694093	0.0000000	9
AMR	method	Beagle - Eagle	0	0.0005949	3.51e-05	1194	16.9440156	0.0000000	9
AMR	method	Beagle - SHAPEIT	0	-0.0005796	3.51e-05	1194	-16.5105705	0.0000000	9
AMR	method	Eagle - SHAPEIT	0	-0.0011745	3.51e-05	1194	-33.4545861	0.0000000	9
EAS	method	Beagle - Eagle	0	0.0007375	4.84e-05	1194	15.2281265	0.0000000	9
EAS	method	Beagle - SHAPEIT	0	-0.0005346	4.84e-05	1194	-11.0390979	0.0000000	9
EAS	method	Eagle - SHAPEIT	0	-0.0012721	4.84e-05	1194	-26.2672245	0.0000000	9
EUR	method	Beagle - Eagle	0	0.0005257	3.97e-05	1194	13.2338941	0.0000000	9
EUR	method	Beagle - SHAPEIT	0	-0.0003380	3.97e-05	1194	-8.5076843	0.0000000	9
EUR	method	Eagle - SHAPEIT	0	-0.0008637	3.97e-05	1194	-21.7415784	0.0000000	9
SAS	method	Beagle - Eagle	0	0.0008345	4.46e-05	1194	18.7234833	0.0000000	9
SAS	method	Beagle - SHAPEIT	0	-0.0006681	4.46e-05	1194	-14.9905111	0.0000000	9
SAS	method	Eagle - SHAPEIT	0	-0.0015027	4.46e-05	1194	-33.7139944	0.0000000	9
AFR	method	Beagle - Eagle	0	0.0009361	2.73e-05	1194	34.3517583	0.0000000	10
AFR	method	Beagle - SHAPEIT	0	-0.0004540	2.73e-05	1194	-16.6621745	0.0000000	10
AFR	method	Eagle - SHAPEIT	0	-0.0013901	2.73e-05	1194	-51.0139328	0.0000000	10
AMR	method	Beagle - Eagle	0	0.0005421	3.30e-05	1194	16.4240841	0.0000000	10
AMR	method	Beagle - SHAPEIT	0	-0.0005065	3.30e-05	1194	-15.3439172	0.0000000	10
AMR	method	Eagle - SHAPEIT	0	-0.0010486	3.30e-05	1194	-31.7680013	0.0000000	10
EAS	method	Beagle - Eagle	0	0.0006121	4.55e-05	1194	13.4448458	0.0000000	10
EAS	method	Beagle - SHAPEIT	0	-0.0005552	4.55e-05	1194	-12.1934201	0.0000000	10
EAS	method	Eagle - SHAPEIT	0	-0.0011673	4.55e-05	1194	-25.6382660	0.0000000	10
EUR	method	Beagle - Eagle	0	0.0004820	3.73e-05	1194	12.9047204	0.0000000	10
EUR	method	Beagle - SHAPEIT	0	-0.0003389	3.73e-05	1194	-9.0728078	0.0000000	10
EUR	method	Eagle - SHAPEIT	0	-0.0008208	3.73e-05	1194	-21.9775282	0.0000000	10
SAS	method	Beagle - Eagle	0	0.0006988	4.19e-05	1194	16.6755787	0.0000000	10
SAS	method	Beagle - SHAPEIT	0	-0.0006227	4.19e-05	1194	-14.8589263	0.0000000	10
SAS	method	Eagle - SHAPEIT	0	-0.0013214	4.19e-05	1194	-31.5345050	0.0000000	10
AFR	method	Beagle - Eagle	0	0.0009588	2.91e-05	1194	32.9384553	0.0000000	11
AFR	method	Beagle - SHAPEIT	0	-0.0004442	2.91e-05	1194	-15.2588026	0.0000000	11
AFR	method	Eagle - SHAPEIT	0	-0.0014030	2.91e-05	1194	-48.1972579	0.0000000	11
AMR	method	Beagle - Eagle	0	0.0005846	3.53e-05	1194	16.5804633	0.0000000	11
AMR	method	Beagle - SHAPEIT	0	-0.0004818	3.53e-05	1194	-13.6655230	0.0000000	11
AMR	method	Eagle - SHAPEIT	0	-0.0010664	3.53e-05	1194	-30.2459863	0.0000000	11
EAS	method	Beagle - Eagle	0	0.0006792	4.86e-05	1194	13.9649322	0.0000000	11
EAS	method	Beagle - SHAPEIT	0	-0.0005654	4.86e-05	1194	-11.6244214	0.0000000	11
EAS	method	Eagle - SHAPEIT	0	-0.0012445	4.86e-05	1194	-25.5893536	0.0000000	11
EUR	method	Beagle - Eagle	0	0.0004581	3.99e-05	1194	11.4830061	0.0000000	11
EUR	method	Beagle - SHAPEIT	0	-0.0003449	3.99e-05	1194	-8.6454033	0.0000000	11
EUR	method	Eagle - SHAPEIT	0	-0.0008030	3.99e-05	1194	-20.1284095	0.0000000	11
SAS	method	Beagle - Eagle	0	0.0007981	4.48e-05	1194	17.8298992	0.0000000	11
SAS	method	Beagle - SHAPEIT	0	-0.0005758	4.48e-05	1194	-12.8646792	0.0000000	11
SAS	method	Eagle - SHAPEIT	0	-0.0013739	4.48e-05	1194	-30.6945783	0.0000000	11
AFR	method	Beagle - Eagle	0	0.0009805	2.94e-05	1194	33.3456546	0.0000000	12
AFR	method	Beagle - SHAPEIT	0	-0.0004469	2.94e-05	1194	-15.1973596	0.0000000	12
AFR	method	Eagle - SHAPEIT	0	-0.0014273	2.94e-05	1194	-48.5430142	0.0000000	12
AMR	method	Beagle - Eagle	0	0.0005527	3.56e-05	1194	15.5188460	0.0000000	12
AMR	method	Beagle - SHAPEIT	0	-0.0005160	3.56e-05	1194	-14.4882119	0.0000000	12
AMR	method	Eagle - SHAPEIT	0	-0.0010687	3.56e-05	1194	-30.0070579	0.0000000	12
EAS	method	Beagle - Eagle	0	0.0006446	4.91e-05	1194	13.1209540	0.0000000	12
EAS	method	Beagle - SHAPEIT	0	-0.0005542	4.91e-05	1194	-11.2813808	0.0000000	12
EAS	method	Eagle - SHAPEIT	0	-0.0011989	4.91e-05	1194	-24.4023348	0.0000000	12
EUR	method	Beagle - Eagle	0	0.0004945	4.03e-05	1194	12.2707447	0.0000000	12
EUR	method	Beagle - SHAPEIT	0	-0.0003928	4.03e-05	1194	-9.7460039	0.0000000	12
EUR	method	Eagle - SHAPEIT	0	-0.0008873	4.03e-05	1194	-22.0167485	0.0000000	12
SAS	method	Beagle - Eagle	0	0.0008702	4.52e-05	1194	19.2460888	0.0000000	12
SAS	method	Beagle - SHAPEIT	0	-0.0006976	4.52e-05	1194	-15.4274222	0.0000000	12
SAS	method	Eagle - SHAPEIT	0	-0.0015678	4.52e-05	1194	-34.6735111	0.0000000	12
AFR	method	Beagle - Eagle	0	0.0009494	3.37e-05	1194	28.1796848	0.0000000	13
AFR	method	Beagle - SHAPEIT	0	-0.0004423	3.37e-05	1194	-13.1289115	0.0000000	13
AFR	method	Eagle - SHAPEIT	0	-0.0013918	3.37e-05	1194	-41.3085963	0.0000000	13
AMR	method	Beagle - Eagle	0	0.0006155	4.08e-05	1194	15.0829186	0.0000000	13
AMR	method	Beagle - SHAPEIT	0	-0.0005177	4.08e-05	1194	-12.6859367	0.0000000	13
AMR	method	Eagle - SHAPEIT	0	-0.0011332	4.08e-05	1194	-27.7688553	0.0000000	13
EAS	method	Beagle - Eagle	0	0.0006017	5.63e-05	1194	10.6882067	0.0000000	13
EAS	method	Beagle - SHAPEIT	0	-0.0005137	5.63e-05	1194	-9.1248408	0.0000000	13
EAS	method	Eagle - SHAPEIT	0	-0.0011153	5.63e-05	1194	-19.8130475	0.0000000	13
EUR	method	Beagle - Eagle	0	0.0005105	4.62e-05	1194	11.0549581	0.0000000	13
EUR	method	Beagle - SHAPEIT	0	-0.0003295	4.62e-05	1194	-7.1348827	0.0000000	13
EUR	method	Eagle - SHAPEIT	0	-0.0008400	4.62e-05	1194	-18.1898408	0.0000000	13
SAS	method	Beagle - Eagle	0	0.0005706	5.18e-05	1194	11.0132829	0.0000000	13
SAS	method	Beagle - SHAPEIT	0	-0.0006886	5.18e-05	1194	-13.2912596	0.0000000	13
SAS	method	Eagle - SHAPEIT	0	-0.0012592	5.18e-05	1194	-24.3045425	0.0000000	13
AFR	method	Beagle - Eagle	0	0.0009366	3.23e-05	1194	29.0277377	0.0000000	14
AFR	method	Beagle - SHAPEIT	0	-0.0004754	3.23e-05	1194	-14.7358601	0.0000000	14
AFR	method	Eagle - SHAPEIT	0	-0.0014120	3.23e-05	1194	-43.7635978	0.0000000	14
AMR	method	Beagle - Eagle	0	0.0006184	3.91e-05	1194	15.8231990	0.0000000	14
AMR	method	Beagle - SHAPEIT	0	-0.0005319	3.91e-05	1194	-13.6113316	0.0000000	14
AMR	method	Eagle - SHAPEIT	0	-0.0011503	3.91e-05	1194	-29.4345306	0.0000000	14
EAS	method	Beagle - Eagle	0	0.0005311	5.39e-05	1194	9.8515468	0.0000000	14
EAS	method	Beagle - SHAPEIT	0	-0.0006087	5.39e-05	1194	-11.2908917	0.0000000	14
EAS	method	Eagle - SHAPEIT	0	-0.0011398	5.39e-05	1194	-21.1424385	0.0000000	14
EUR	method	Beagle - Eagle	0	0.0004178	4.42e-05	1194	9.4470466	0.0000000	14
EUR	method	Beagle - SHAPEIT	0	-0.0004479	4.42e-05	1194	-10.1290810	0.0000000	14
EUR	method	Eagle - SHAPEIT	0	-0.0008657	4.42e-05	1194	-19.5761276	0.0000000	14
SAS	method	Beagle - Eagle	0	0.0007671	4.96e-05	1194	15.4608902	0.0000000	14
SAS	method	Beagle - SHAPEIT	0	-0.0006599	4.96e-05	1194	-13.2999178	0.0000000	14
SAS	method	Eagle - SHAPEIT	0	-0.0014270	4.96e-05	1194	-28.7608080	0.0000000	14
AFR	method	Beagle - Eagle	0	0.0009330	3.37e-05	1194	27.7137999	0.0000000	15
AFR	method	Beagle - SHAPEIT	0	-0.0004976	3.37e-05	1194	-14.7796766	0.0000000	15
AFR	method	Eagle - SHAPEIT	0	-0.0014306	3.37e-05	1194	-42.4934765	0.0000000	15
AMR	method	Beagle - Eagle	0	0.0006078	4.08e-05	1194	14.9045348	0.0000000	15
AMR	method	Beagle - SHAPEIT	0	-0.0005884	4.08e-05	1194	-14.4299566	0.0000000	15
AMR	method	Eagle - SHAPEIT	0	-0.0011962	4.08e-05	1194	-29.3344915	0.0000000	15
EAS	method	Beagle - Eagle	0	0.0006875	5.63e-05	1194	12.2219924	0.0000000	15
EAS	method	Beagle - SHAPEIT	0	-0.0006197	5.63e-05	1194	-11.0173355	0.0000000	15
EAS	method	Eagle - SHAPEIT	0	-0.0013072	5.63e-05	1194	-23.2393278	0.0000000	15
EUR	method	Beagle - Eagle	0	0.0004948	4.61e-05	1194	10.7222326	0.0000000	15
EUR	method	Beagle - SHAPEIT	0	-0.0004012	4.61e-05	1194	-8.6953236	0.0000000	15
EUR	method	Eagle - SHAPEIT	0	-0.0008960	4.61e-05	1194	-19.4175562	0.0000000	15
SAS	method	Beagle - Eagle	0	0.0007174	5.18e-05	1194	13.8571011	0.0000000	15
SAS	method	Beagle - SHAPEIT	0	-0.0007714	5.18e-05	1194	-14.9000610	0.0000000	15
SAS	method	Eagle - SHAPEIT	0	-0.0014888	5.18e-05	1194	-28.7571621	0.0000000	15
AFR	method	Beagle - Eagle	0	0.0010336	3.98e-05	1194	25.9845228	0.0000000	16
AFR	method	Beagle - SHAPEIT	0	-0.0005083	3.98e-05	1194	-12.7796384	0.0000000	16
AFR	method	Eagle - SHAPEIT	0	-0.0015419	3.98e-05	1194	-38.7641612	0.0000000	16
AMR	method	Beagle - Eagle	0	0.0007562	4.82e-05	1194	15.6958664	0.0000000	16
AMR	method	Beagle - SHAPEIT	0	-0.0005972	4.82e-05	1194	-12.3948802	0.0000000	16
AMR	method	Eagle - SHAPEIT	0	-0.0013534	4.82e-05	1194	-28.0907466	0.0000000	16
EAS	method	Beagle - Eagle	0	0.0008779	6.65e-05	1194	13.2097841	0.0000000	16
EAS	method	Beagle - SHAPEIT	0	-0.0005257	6.65e-05	1194	-7.9102447	0.0000000	16
EAS	method	Eagle - SHAPEIT	0	-0.0014036	6.65e-05	1194	-21.1200288	0.0000000	16
EUR	method	Beagle - Eagle	0	0.0004868	5.45e-05	1194	8.9291526	0.0000000	16
EUR	method	Beagle - SHAPEIT	0	-0.0005622	5.45e-05	1194	-10.3117112	0.0000000	16
EUR	method	Eagle - SHAPEIT	0	-0.0010490	5.45e-05	1194	-19.2408638	0.0000000	16
SAS	method	Beagle - Eagle	0	0.0011418	6.12e-05	1194	18.6669233	0.0000000	16
SAS	method	Beagle - SHAPEIT	0	-0.0005952	6.12e-05	1194	-9.7305849	0.0000000	16
SAS	method	Eagle - SHAPEIT	0	-0.0017370	6.12e-05	1194	-28.3975082	0.0000000	16
AFR	method	Beagle - Eagle	0	0.0009037	3.79e-05	1194	23.8142970	0.0000000	17
AFR	method	Beagle - SHAPEIT	0	-0.0005704	3.79e-05	1194	-15.0312054	0.0000000	17
AFR	method	Eagle - SHAPEIT	0	-0.0014741	3.79e-05	1194	-38.8455023	0.0000000	17
AMR	method	Beagle - Eagle	0	0.0006554	4.60e-05	1194	14.2596925	0.0000000	17
AMR	method	Beagle - SHAPEIT	0	-0.0005576	4.60e-05	1194	-12.1300782	0.0000000	17
AMR	method	Eagle - SHAPEIT	0	-0.0012130	4.60e-05	1194	-26.3897707	0.0000000	17
EAS	method	Beagle - Eagle	0	0.0007784	6.34e-05	1194	12.2766615	0.0000000	17
EAS	method	Beagle - SHAPEIT	0	-0.0004861	6.34e-05	1194	-7.6671341	0.0000000	17
EAS	method	Eagle - SHAPEIT	0	-0.0012645	6.34e-05	1194	-19.9437956	0.0000000	17
EUR	method	Beagle - Eagle	0	0.0005344	5.20e-05	1194	10.2753905	0.0000000	17
EUR	method	Beagle - SHAPEIT	0	-0.0004193	5.20e-05	1194	-8.0618827	0.0000000	17
EUR	method	Eagle - SHAPEIT	0	-0.0009537	5.20e-05	1194	-18.3372732	0.0000000	17
SAS	method	Beagle - Eagle	0	0.0007848	5.84e-05	1194	13.4487008	0.0000000	17
SAS	method	Beagle - SHAPEIT	0	-0.0007282	5.84e-05	1194	-12.4784645	0.0000000	17
SAS	method	Eagle - SHAPEIT	0	-0.0015130	5.84e-05	1194	-25.9271653	0.0000000	17
AFR	method	Beagle - Eagle	0	0.0009311	3.27e-05	1194	28.4332267	0.0000000	18
AFR	method	Beagle - SHAPEIT	0	-0.0005011	3.27e-05	1194	-15.3030643	0.0000000	18
AFR	method	Eagle - SHAPEIT	0	-0.0014322	3.27e-05	1194	-43.7362910	0.0000000	18
AMR	method	Beagle - Eagle	0	0.0006152	3.97e-05	1194	15.5104234	0.0000000	18
AMR	method	Beagle - SHAPEIT	0	-0.0005582	3.97e-05	1194	-14.0743641	0.0000000	18
AMR	method	Eagle - SHAPEIT	0	-0.0011735	3.97e-05	1194	-29.5847874	0.0000000	18
EAS	method	Beagle - Eagle	0	0.0006572	5.47e-05	1194	12.0110972	0.0000000	18
EAS	method	Beagle - SHAPEIT	0	-0.0004812	5.47e-05	1194	-8.7954706	0.0000000	18
EAS	method	Eagle - SHAPEIT	0	-0.0011384	5.47e-05	1194	-20.8065678	0.0000000	18
EUR	method	Beagle - Eagle	0	0.0004612	4.49e-05	1194	10.2768356	0.0000000	18
EUR	method	Beagle - SHAPEIT	0	-0.0003517	4.49e-05	1194	-7.8361100	0.0000000	18
EUR	method	Eagle - SHAPEIT	0	-0.0008129	4.49e-05	1194	-18.1129456	0.0000000	18
SAS	method	Beagle - Eagle	0	0.0008077	5.04e-05	1194	16.0393063	0.0000000	18
SAS	method	Beagle - SHAPEIT	0	-0.0006238	5.04e-05	1194	-12.3879880	0.0000000	18
SAS	method	Eagle - SHAPEIT	0	-0.0014315	5.04e-05	1194	-28.4272943	0.0000000	18
AFR	method	Beagle - Eagle	0	0.0009500	3.77e-05	1194	25.1730555	0.0000000	19
AFR	method	Beagle - SHAPEIT	0	-0.0004197	3.77e-05	1194	-11.1219244	0.0000000	19
AFR	method	Eagle - SHAPEIT	0	-0.0013697	3.77e-05	1194	-36.2949798	0.0000000	19
AMR	method	Beagle - Eagle	0	0.0005645	4.57e-05	1194	12.3499532	0.0000000	19
AMR	method	Beagle - SHAPEIT	0	-0.0004922	4.57e-05	1194	-10.7689680	0.0000000	19
AMR	method	Eagle - SHAPEIT	0	-0.0010567	4.57e-05	1194	-23.1189212	0.0000000	19
EAS	method	Beagle - Eagle	0	0.0007675	6.31e-05	1194	12.1723495	0.0000000	19
EAS	method	Beagle - SHAPEIT	0	-0.0005041	6.31e-05	1194	-7.9943179	0.0000000	19
EAS	method	Eagle - SHAPEIT	0	-0.0012715	6.31e-05	1194	-20.1666674	0.0000000	19
EUR	method	Beagle - Eagle	0	0.0005255	5.17e-05	1194	10.1592207	0.0000000	19
EUR	method	Beagle - SHAPEIT	0	-0.0003221	5.17e-05	1194	-6.2279019	0.0000000	19
EUR	method	Eagle - SHAPEIT	0	-0.0008476	5.17e-05	1194	-16.3871226	0.0000000	19
SAS	method	Beagle - Eagle	0	0.0008199	5.80e-05	1194	14.1290024	0.0000000	19
SAS	method	Beagle - SHAPEIT	0	-0.0006057	5.80e-05	1194	-10.4371748	0.0000000	19
SAS	method	Eagle - SHAPEIT	0	-0.0014256	5.80e-05	1194	-24.5661771	0.0000000	19
AFR	method	Beagle - Eagle	0	0.0009503	3.76e-05	1194	25.2430068	0.0000000	20
AFR	method	Beagle - SHAPEIT	0	-0.0004275	3.76e-05	1194	-11.3546946	0.0000000	20
AFR	method	Eagle - SHAPEIT	0	-0.0013778	3.76e-05	1194	-36.5977015	0.0000000	20
AMR	method	Beagle - Eagle	0	0.0006303	4.56e-05	1194	13.8225493	0.0000000	20
AMR	method	Beagle - SHAPEIT	0	-0.0005541	4.56e-05	1194	-12.1503575	0.0000000	20
AMR	method	Eagle - SHAPEIT	0	-0.0011844	4.56e-05	1194	-25.9729068	0.0000000	20
EAS	method	Beagle - Eagle	0	0.0006016	6.29e-05	1194	9.5633759	0.0000000	20
EAS	method	Beagle - SHAPEIT	0	-0.0006022	6.29e-05	1194	-9.5734425	0.0000000	20
EAS	method	Eagle - SHAPEIT	0	-0.0012037	6.29e-05	1194	-19.1368184	0.0000000	20
EUR	method	Beagle - Eagle	0	0.0004010	5.16e-05	1194	7.7713077	0.0000000	20
EUR	method	Beagle - SHAPEIT	0	-0.0004030	5.16e-05	1194	-7.8097288	0.0000000	20
EUR	method	Eagle - SHAPEIT	0	-0.0008040	5.16e-05	1194	-15.5810365	0.0000000	20
SAS	method	Beagle - Eagle	0	0.0007963	5.79e-05	1194	13.7553409	0.0000000	20
SAS	method	Beagle - SHAPEIT	0	-0.0005950	5.79e-05	1194	-10.2781881	0.0000000	20
SAS	method	Eagle - SHAPEIT	0	-0.0013913	5.79e-05	1194	-24.0335290	0.0000000	20
AFR	method	Beagle - Eagle	0	0.0007936	4.27e-05	1194	18.6063616	0.0000000	21
AFR	method	Beagle - SHAPEIT	0	-0.0005259	4.27e-05	1194	-12.3286685	0.0000000	21
AFR	method	Eagle - SHAPEIT	0	-0.0013195	4.27e-05	1194	-30.9350301	0.0000000	21
AMR	method	Beagle - Eagle	0	0.0004138	5.17e-05	1194	8.0095312	0.0000000	21
AMR	method	Beagle - SHAPEIT	0	-0.0005427	5.17e-05	1194	-10.5038851	0.0000000	21
AMR	method	Eagle - SHAPEIT	0	-0.0009565	5.17e-05	1194	-18.5134163	0.0000000	21
EAS	method	Beagle - Eagle	0	0.0006084	7.13e-05	1194	8.5367065	0.0000000	21
EAS	method	Beagle - SHAPEIT	0	-0.0004902	7.13e-05	1194	-6.8790138	0.0000000	21
EAS	method	Eagle - SHAPEIT	0	-0.0010986	7.13e-05	1194	-15.4157203	0.0000000	21
EUR	method	Beagle - Eagle	0	0.0004332	5.85e-05	1194	7.4102562	0.0000000	21
EUR	method	Beagle - SHAPEIT	0	-0.0004457	5.85e-05	1194	-7.6247750	0.0000000	21
EUR	method	Eagle - SHAPEIT	0	-0.0008789	5.85e-05	1194	-15.0350312	0.0000000	21
SAS	method	Beagle - Eagle	0	0.0006113	6.56e-05	1194	9.3201362	0.0000000	21
SAS	method	Beagle - SHAPEIT	0	-0.0006490	6.56e-05	1194	-9.8951103	0.0000000	21
SAS	method	Eagle - SHAPEIT	0	-0.0012603	6.56e-05	1194	-19.2152465	0.0000000	21
AFR	method	Beagle - Eagle	0	0.0008486	4.65e-05	1194	18.2576111	0.0000000	22
AFR	method	Beagle - SHAPEIT	0	-0.0005283	4.65e-05	1194	-11.3668957	0.0000000	22
AFR	method	Eagle - SHAPEIT	0	-0.0013769	4.65e-05	1194	-29.6245069	0.0000000	22
AMR	method	Beagle - Eagle	0	0.0005098	5.63e-05	1194	9.0551190	0.0000000	22
AMR	method	Beagle - SHAPEIT	0	-0.0005420	5.63e-05	1194	-9.6277848	0.0000000	22
AMR	method	Eagle - SHAPEIT	0	-0.0010518	5.63e-05	1194	-18.6829039	0.0000000	22
EAS	method	Beagle - Eagle	0	0.0005407	7.77e-05	1194	6.9627479	0.0000000	22
EAS	method	Beagle - SHAPEIT	0	-0.0005423	7.77e-05	1194	-6.9832513	0.0000000	22
EAS	method	Eagle - SHAPEIT	0	-0.0010830	7.77e-05	1194	-13.9459992	0.0000000	22
EUR	method	Beagle - Eagle	0	0.0003903	6.37e-05	1194	6.1269545	0.0000000	22
EUR	method	Beagle - SHAPEIT	0	-0.0004136	6.37e-05	1194	-6.4927862	0.0000000	22
EUR	method	Eagle - SHAPEIT	0	-0.0008039	6.37e-05	1194	-12.6197407	0.0000000	22
SAS	method	Beagle - Eagle	0	0.0006218	7.15e-05	1194	8.7001914	0.0000000	22
SAS	method	Beagle - SHAPEIT	0	-0.0007412	7.15e-05	1194	-10.3710731	0.0000000	22
SAS	method	Eagle - SHAPEIT	0	-0.0013631	7.15e-05	1194	-19.0712645	0.0000000	22
AFR	method	Beagle - Eagle	0	0.0000090	1.32e-05	1990	0.6832970	0.7732702	23
AFR	method	Beagle - SHAPEIT	0	-0.0001865	1.32e-05	1990	-14.1689679	0.0000000	23
AFR	method	Eagle - SHAPEIT	0	-0.0001955	1.32e-05	1990	-14.8522649	0.0000000	23
AMR	method	Beagle - Eagle	0	0.0000208	1.32e-05	1990	1.5785688	0.2551503	23
AMR	method	Beagle - SHAPEIT	0	-0.0001695	1.32e-05	1990	-12.8743522	0.0000000	23
AMR	method	Eagle - SHAPEIT	0	-0.0001902	1.32e-05	1990	-14.4529210	0.0000000	23
EAS	method	Beagle - Eagle	0	0.0000128	1.32e-05	1990	0.9717229	0.5948612	23
EAS	method	Beagle - SHAPEIT	0	-0.0001560	1.32e-05	1990	-11.8509140	0.0000000	23
EAS	method	Eagle - SHAPEIT	0	-0.0001688	1.32e-05	1990	-12.8226369	0.0000000	23
EUR	method	Beagle - Eagle	0	0.0000119	1.32e-05	1990	0.9049559	0.6372251	23
EUR	method	Beagle - SHAPEIT	0	-0.0001806	1.32e-05	1990	-13.7242659	0.0000000	23
EUR	method	Eagle - SHAPEIT	0	-0.0001925	1.32e-05	1990	-14.6292218	0.0000000	23
SAS	method	Beagle - Eagle	0	-0.0000318	1.32e-05	1990	-2.4127848	0.0420849	23
SAS	method	Beagle - SHAPEIT	0	-0.0002085	1.32e-05	1990	-15.8443297	0.0000000	23
SAS	method	Eagle - SHAPEIT	0	-0.0001768	1.32e-05	1990	-13.4315449	0.0000000	23

df_pop_pop %>% knitr::kable()

method	term	contrast	null.value	estimate	std.error	df	statistic	adj.p.value	chrom
Beagle	SUPER	AFR - AMR	0	-0.0007318	0.0001295	634.6203	-5.6529163	0.0000002	1
Beagle	SUPER	AFR - EAS	0	-0.0026433	0.0001605	634.6203	-16.4701971	0.0000000	1
Beagle	SUPER	AFR - EUR	0	-0.0005607	0.0001398	634.6203	-4.0098589	0.0006479	1
Beagle	SUPER	AFR - SAS	0	-0.0021981	0.0001512	634.6203	-14.5388504	0.0000000	1
Beagle	SUPER	AMR - EAS	0	-0.0019115	0.0001701	634.6203	-11.2381013	0.0000000	1
Beagle	SUPER	AMR - EUR	0	0.0001711	0.0001508	634.6203	1.1349456	0.7879365	1
Beagle	SUPER	AMR - SAS	0	-0.0014662	0.0001613	634.6203	-9.0878937	0.0000000	1
Beagle	SUPER	EAS - EUR	0	0.0020826	0.0001781	634.6203	11.6923806	0.0000000	1
Beagle	SUPER	EAS - SAS	0	0.0004453	0.0001872	634.6203	2.3790629	0.1223711	1
Beagle	SUPER	EUR - SAS	0	-0.0016373	0.0001698	634.6203	-9.6439472	0.0000000	1
Eagle	SUPER	AFR - AMR	0	-0.0011347	0.0001295	634.6203	-8.7646480	0.0000000	1
Eagle	SUPER	AFR - EAS	0	-0.0029467	0.0001605	634.6203	-18.3605031	0.0000000	1
Eagle	SUPER	AFR - EUR	0	-0.0010682	0.0001398	634.6203	-7.6386069	0.0000000	1
Eagle	SUPER	AFR - SAS	0	-0.0023939	0.0001512	634.6203	-15.8340793	0.0000000	1
Eagle	SUPER	AMR - EAS	0	-0.0018120	0.0001701	634.6203	-10.6533194	0.0000000	1
Eagle	SUPER	AMR - EUR	0	0.0000665	0.0001508	634.6203	0.4412002	0.9921352	1
Eagle	SUPER	AMR - SAS	0	-0.0012592	0.0001613	634.6203	-7.8047376	0.0000000	1
Eagle	SUPER	EAS - EUR	0	0.0018786	0.0001781	634.6203	10.5467618	0.0000000	1
Eagle	SUPER	EAS - SAS	0	0.0005528	0.0001872	634.6203	2.9537531	0.0268840	1
Eagle	SUPER	EUR - SAS	0	-0.0013257	0.0001698	634.6203	-7.8085548	0.0000000	1
SHAPEIT	SUPER	AFR - AMR	0	-0.0008525	0.0001295	634.6203	-6.5851335	0.0000000	1
SHAPEIT	SUPER	AFR - EAS	0	-0.0027171	0.0001605	634.6203	-16.9296343	0.0000000	1
SHAPEIT	SUPER	AFR - EUR	0	-0.0004786	0.0001398	634.6203	-3.4223401	0.0059368	1
SHAPEIT	SUPER	AFR - SAS	0	-0.0024242	0.0001512	634.6203	-16.0342603	0.0000000	1
SHAPEIT	SUPER	AMR - EAS	0	-0.0018646	0.0001701	634.6203	-10.9620792	0.0000000	1
SHAPEIT	SUPER	AMR - EUR	0	0.0003739	0.0001508	634.6203	2.4804295	0.0963581	1
SHAPEIT	SUPER	AMR - SAS	0	-0.0015716	0.0001613	634.6203	-9.7411719	0.0000000	1
SHAPEIT	SUPER	EAS - EUR	0	0.0022385	0.0001781	634.6203	12.5676089	0.0000000	1
SHAPEIT	SUPER	EAS - SAS	0	0.0002929	0.0001872	634.6203	1.5650529	0.5204822	1
SHAPEIT	SUPER	EUR - SAS	0	-0.0019456	0.0001698	634.6203	-11.4594888	0.0000000	1
Beagle	SUPER	AFR - AMR	0	-0.0009213	0.0001293	637.2694	-7.1226395	0.0000000	2
Beagle	SUPER	AFR - EAS	0	-0.0027566	0.0001604	637.2694	-17.1909150	0.0000000	2
Beagle	SUPER	AFR - EUR	0	-0.0004559	0.0001397	637.2694	-3.2629891	0.0101862	2
Beagle	SUPER	AFR - SAS	0	-0.0022843	0.0001511	637.2694	-15.1223637	0.0000000	2
Beagle	SUPER	AMR - EAS	0	-0.0018353	0.0001699	637.2694	-10.7995069	0.0000000	2
Beagle	SUPER	AMR - EUR	0	0.0004654	0.0001506	637.2694	3.0898106	0.0177665	2
Beagle	SUPER	AMR - SAS	0	-0.0013630	0.0001612	637.2694	-8.4553700	0.0000000	2
Beagle	SUPER	EAS - EUR	0	0.0023007	0.0001780	637.2694	12.9281400	0.0000000	2
Beagle	SUPER	EAS - SAS	0	0.0004723	0.0001870	637.2694	2.5257317	0.0862447	2
Beagle	SUPER	EUR - SAS	0	-0.0018284	0.0001696	637.2694	-10.7787067	0.0000000	2
Eagle	SUPER	AFR - AMR	0	-0.0012853	0.0001293	637.2694	-9.9369481	0.0000000	2
Eagle	SUPER	AFR - EAS	0	-0.0030943	0.0001604	637.2694	-19.2970026	0.0000000	2
Eagle	SUPER	AFR - EUR	0	-0.0009408	0.0001397	637.2694	-6.7334498	0.0000000	2
Eagle	SUPER	AFR - SAS	0	-0.0024193	0.0001511	637.2694	-16.0162249	0.0000000	2
Eagle	SUPER	AMR - EAS	0	-0.0018090	0.0001699	637.2694	-10.6447030	0.0000000	2
Eagle	SUPER	AMR - EUR	0	0.0003446	0.0001506	637.2694	2.2874798	0.1502244	2
Eagle	SUPER	AMR - SAS	0	-0.0011340	0.0001612	637.2694	-7.0347607	0.0000000	2
Eagle	SUPER	EAS - EUR	0	0.0021535	0.0001780	637.2694	12.1012202	0.0000000	2
Eagle	SUPER	EAS - SAS	0	0.0006750	0.0001870	637.2694	3.6096813	0.0030410	2
Eagle	SUPER	EUR - SAS	0	-0.0014786	0.0001696	637.2694	-8.7162740	0.0000000	2
SHAPEIT	SUPER	AFR - AMR	0	-0.0009785	0.0001293	637.2694	-7.5645959	0.0000000	2
SHAPEIT	SUPER	AFR - EAS	0	-0.0029484	0.0001604	637.2694	-18.3871557	0.0000000	2
SHAPEIT	SUPER	AFR - EUR	0	-0.0004042	0.0001397	637.2694	-2.8930653	0.0321198	2
SHAPEIT	SUPER	AFR - SAS	0	-0.0024738	0.0001511	637.2694	-16.3768429	0.0000000	2
SHAPEIT	SUPER	AMR - EAS	0	-0.0019700	0.0001699	637.2694	-11.5918520	0.0000000	2
SHAPEIT	SUPER	AMR - EUR	0	0.0005743	0.0001506	637.2694	3.8124594	0.0014166	2
SHAPEIT	SUPER	AMR - SAS	0	-0.0014953	0.0001612	637.2694	-9.2762684	0.0000000	2
SHAPEIT	SUPER	EAS - EUR	0	0.0025442	0.0001780	637.2694	14.2964339	0.0000000	2
SHAPEIT	SUPER	EAS - SAS	0	0.0004746	0.0001870	637.2694	2.5381662	0.0836247	2
SHAPEIT	SUPER	EUR - SAS	0	-0.0020696	0.0001696	637.2694	-12.2004839	0.0000000	2
Beagle	SUPER	AFR - AMR	0	-0.0007966	0.0001254	635.7836	-6.3515083	0.0000000	3
Beagle	SUPER	AFR - EAS	0	-0.0026264	0.0001555	635.7836	-16.8917081	0.0000000	3
Beagle	SUPER	AFR - EUR	0	-0.0005786	0.0001355	635.7836	-4.2707710	0.0002173	3
Beagle	SUPER	AFR - SAS	0	-0.0020990	0.0001465	635.7836	-14.3307780	0.0000000	3
Beagle	SUPER	AMR - EAS	0	-0.0018298	0.0001648	635.7836	-11.1041104	0.0000000	3
Beagle	SUPER	AMR - EUR	0	0.0002180	0.0001461	635.7836	1.4928364	0.5675191	3
Beagle	SUPER	AMR - SAS	0	-0.0013024	0.0001563	635.7836	-8.3323635	0.0000000	3
Beagle	SUPER	EAS - EUR	0	0.0020478	0.0001726	635.7836	11.8673446	0.0000000	3
Beagle	SUPER	EAS - SAS	0	0.0005274	0.0001813	635.7836	2.9085959	0.0307031	3
Beagle	SUPER	EUR - SAS	0	-0.0015204	0.0001645	635.7836	-9.2437650	0.0000000	3
Eagle	SUPER	AFR - AMR	0	-0.0011999	0.0001254	635.7836	-9.5666227	0.0000000	3
Eagle	SUPER	AFR - EAS	0	-0.0029595	0.0001555	635.7836	-19.0338487	0.0000000	3
Eagle	SUPER	AFR - EUR	0	-0.0011011	0.0001355	635.7836	-8.1274319	0.0000000	3
Eagle	SUPER	AFR - SAS	0	-0.0023125	0.0001465	635.7836	-15.7885370	0.0000000	3
Eagle	SUPER	AMR - EAS	0	-0.0017596	0.0001648	635.7836	-10.6782633	0.0000000	3
Eagle	SUPER	AMR - EUR	0	0.0000988	0.0001461	635.7836	0.6764657	0.9614685	3
Eagle	SUPER	AMR - SAS	0	-0.0011127	0.0001563	635.7836	-7.1185536	0.0000000	3
Eagle	SUPER	EAS - EUR	0	0.0018584	0.0001726	635.7836	10.7697101	0.0000000	3
Eagle	SUPER	EAS - SAS	0	0.0006469	0.0001813	635.7836	3.5679475	0.0035411	3
Eagle	SUPER	EUR - SAS	0	-0.0012115	0.0001645	635.7836	-7.3653855	0.0000000	3
SHAPEIT	SUPER	AFR - AMR	0	-0.0008649	0.0001254	635.7836	-6.8958807	0.0000000	3
SHAPEIT	SUPER	AFR - EAS	0	-0.0026849	0.0001555	635.7836	-17.2682319	0.0000000	3
SHAPEIT	SUPER	AFR - EUR	0	-0.0004916	0.0001355	635.7836	-3.6290189	0.0028329	3
SHAPEIT	SUPER	AFR - SAS	0	-0.0022789	0.0001465	635.7836	-15.5589179	0.0000000	3
SHAPEIT	SUPER	AMR - EAS	0	-0.0018200	0.0001648	635.7836	-11.0450509	0.0000000	3
SHAPEIT	SUPER	AMR - EUR	0	0.0003732	0.0001461	635.7836	2.5555705	0.0800688	3
SHAPEIT	SUPER	AMR - SAS	0	-0.0014140	0.0001563	635.7836	-9.0464011	0.0000000	3
SHAPEIT	SUPER	EAS - EUR	0	0.0021933	0.0001726	635.7836	12.7104415	0.0000000	3
SHAPEIT	SUPER	EAS - SAS	0	0.0004060	0.0001813	635.7836	2.2393857	0.1666180	3
SHAPEIT	SUPER	EUR - SAS	0	-0.0017873	0.0001645	635.7836	-10.8659754	0.0000000	3
Beagle	SUPER	AFR - AMR	0	-0.0009254	0.0001150	646.7191	-8.0490906	0.0000000	4
Beagle	SUPER	AFR - EAS	0	-0.0023588	0.0001425	646.7191	-16.5501304	0.0000000	4
Beagle	SUPER	AFR - EUR	0	-0.0005374	0.0001242	646.7191	-4.3278569	0.0001692	4
Beagle	SUPER	AFR - SAS	0	-0.0020837	0.0001343	646.7191	-15.5199665	0.0000000	4
Beagle	SUPER	AMR - EAS	0	-0.0014334	0.0001511	646.7191	-9.4897459	0.0000000	4
Beagle	SUPER	AMR - EUR	0	0.0003879	0.0001339	646.7191	2.8976528	0.0316821	4
Beagle	SUPER	AMR - SAS	0	-0.0011583	0.0001433	646.7191	-8.0845605	0.0000000	4
Beagle	SUPER	EAS - EUR	0	0.0018214	0.0001582	646.7191	11.5147488	0.0000000	4
Beagle	SUPER	EAS - SAS	0	0.0002751	0.0001662	646.7191	1.6550659	0.4627529	4
Beagle	SUPER	EUR - SAS	0	-0.0015463	0.0001508	646.7191	-10.2557006	0.0000000	4
Eagle	SUPER	AFR - AMR	0	-0.0013097	0.0001150	646.7191	-11.3916004	0.0000000	4
Eagle	SUPER	AFR - EAS	0	-0.0027357	0.0001425	646.7191	-19.1944371	0.0000000	4
Eagle	SUPER	AFR - EUR	0	-0.0009896	0.0001242	646.7191	-7.9687864	0.0000000	4
Eagle	SUPER	AFR - SAS	0	-0.0022520	0.0001343	646.7191	-16.7735518	0.0000000	4
Eagle	SUPER	AMR - EAS	0	-0.0014260	0.0001511	646.7191	-9.4407604	0.0000000	4
Eagle	SUPER	AMR - EUR	0	0.0003201	0.0001339	646.7191	2.3907847	0.1190861	4
Eagle	SUPER	AMR - SAS	0	-0.0009424	0.0001433	646.7191	-6.5772043	0.0000000	4
Eagle	SUPER	EAS - EUR	0	0.0017461	0.0001582	646.7191	11.0389585	0.0000000	4
Eagle	SUPER	EAS - SAS	0	0.0004837	0.0001662	646.7191	2.9099644	0.0305661	4
Eagle	SUPER	EUR - SAS	0	-0.0012625	0.0001508	646.7191	-8.3731921	0.0000000	4
SHAPEIT	SUPER	AFR - AMR	0	-0.0010420	0.0001150	646.7191	-9.0637005	0.0000000	4
SHAPEIT	SUPER	AFR - EAS	0	-0.0025324	0.0001425	646.7191	-17.7682398	0.0000000	4
SHAPEIT	SUPER	AFR - EUR	0	-0.0004991	0.0001242	646.7191	-4.0188066	0.0006235	4
SHAPEIT	SUPER	AFR - SAS	0	-0.0022172	0.0001343	646.7191	-16.5138367	0.0000000	4
SHAPEIT	SUPER	AMR - EAS	0	-0.0014904	0.0001511	646.7191	-9.8668672	0.0000000	4
SHAPEIT	SUPER	AMR - EUR	0	0.0005430	0.0001339	646.7191	4.0555932	0.0005364	4
SHAPEIT	SUPER	AMR - SAS	0	-0.0011751	0.0001433	646.7191	-8.2017520	0.0000000	4
SHAPEIT	SUPER	EAS - EUR	0	0.0020334	0.0001582	646.7191	12.8549567	0.0000000	4
SHAPEIT	SUPER	EAS - SAS	0	0.0003153	0.0001662	646.7191	1.8967721	0.3200442	4
SHAPEIT	SUPER	EUR - SAS	0	-0.0017181	0.0001508	646.7191	-11.3952718	0.0000000	4
Beagle	SUPER	AFR - AMR	0	-0.0006740	0.0001304	637.7817	-5.1704390	0.0000031	5
Beagle	SUPER	AFR - EAS	0	-0.0025078	0.0001616	637.7817	-15.5185523	0.0000000	5
Beagle	SUPER	AFR - EUR	0	-0.0004742	0.0001408	637.7817	-3.3680775	0.0071550	5
Beagle	SUPER	AFR - SAS	0	-0.0021772	0.0001522	637.7817	-14.3018027	0.0000000	5
Beagle	SUPER	AMR - EAS	0	-0.0018338	0.0001713	637.7817	-10.7073889	0.0000000	5
Beagle	SUPER	AMR - EUR	0	0.0001998	0.0001518	637.7817	1.3159190	0.6814036	5
Beagle	SUPER	AMR - SAS	0	-0.0015032	0.0001625	637.7817	-9.2529070	0.0000000	5
Beagle	SUPER	EAS - EUR	0	0.0020336	0.0001793	637.7817	11.3387550	0.0000000	5
Beagle	SUPER	EAS - SAS	0	0.0003306	0.0001885	637.7817	1.7544970	0.4013676	5
Beagle	SUPER	EUR - SAS	0	-0.0017029	0.0001710	637.7817	-9.9614553	0.0000000	5
Eagle	SUPER	AFR - AMR	0	-0.0011415	0.0001304	637.7817	-8.7568075	0.0000000	5
Eagle	SUPER	AFR - EAS	0	-0.0028415	0.0001616	637.7817	-17.5836014	0.0000000	5
Eagle	SUPER	AFR - EUR	0	-0.0009759	0.0001408	637.7817	-6.9311149	0.0000000	5
Eagle	SUPER	AFR - SAS	0	-0.0023625	0.0001522	637.7817	-15.5191769	0.0000000	5
Eagle	SUPER	AMR - EAS	0	-0.0017000	0.0001713	637.7817	-9.9262320	0.0000000	5
Eagle	SUPER	AMR - EUR	0	0.0001656	0.0001518	637.7817	1.0907097	0.8113679	5
Eagle	SUPER	AMR - SAS	0	-0.0012210	0.0001625	637.7817	-7.5159454	0.0000000	5
Eagle	SUPER	EAS - EUR	0	0.0018656	0.0001793	637.7817	10.4021768	0.0000000	5
Eagle	SUPER	EAS - SAS	0	0.0004790	0.0001885	637.7817	2.5419231	0.0828449	5
Eagle	SUPER	EUR - SAS	0	-0.0013866	0.0001710	637.7817	-8.1108562	0.0000000	5
SHAPEIT	SUPER	AFR - AMR	0	-0.0007978	0.0001304	637.7817	-6.1204913	0.0000000	5
SHAPEIT	SUPER	AFR - EAS	0	-0.0026962	0.0001616	637.7817	-16.6846301	0.0000000	5
SHAPEIT	SUPER	AFR - EUR	0	-0.0003933	0.0001408	637.7817	-2.7935710	0.0426224	5
SHAPEIT	SUPER	AFR - SAS	0	-0.0023583	0.0001522	637.7817	-15.4915609	0.0000000	5
SHAPEIT	SUPER	AMR - EAS	0	-0.0018984	0.0001713	637.7817	-11.0845512	0.0000000	5
SHAPEIT	SUPER	AMR - EUR	0	0.0004045	0.0001518	637.7817	2.6646487	0.0604675	5
SHAPEIT	SUPER	AMR - SAS	0	-0.0015605	0.0001625	637.7817	-9.6054592	0.0000000	5
SHAPEIT	SUPER	EAS - EUR	0	0.0023029	0.0001793	637.7817	12.8404856	0.0000000	5
SHAPEIT	SUPER	EAS - SAS	0	0.0003380	0.0001885	637.7817	1.7933476	0.3783077	5
SHAPEIT	SUPER	EUR - SAS	0	-0.0019649	0.0001710	637.7817	-11.4941014	0.0000000	5
Beagle	SUPER	AFR - AMR	0	-0.0006305	0.0001157	637.8403	-5.4492722	0.0000007	6
Beagle	SUPER	AFR - EAS	0	-0.0022255	0.0001434	637.8403	-15.5161836	0.0000000	6
Beagle	SUPER	AFR - EUR	0	-0.0003023	0.0001250	637.8403	-2.4193871	0.1114328	6
Beagle	SUPER	AFR - SAS	0	-0.0018604	0.0001351	637.8403	-13.7691065	0.0000000	6
Beagle	SUPER	AMR - EAS	0	-0.0015950	0.0001520	637.8403	-10.4929281	0.0000000	6
Beagle	SUPER	AMR - EUR	0	0.0003281	0.0001347	637.8403	2.4353303	0.1073266	6
Beagle	SUPER	AMR - SAS	0	-0.0012299	0.0001442	637.8403	-8.5300001	0.0000000	6
Beagle	SUPER	EAS - EUR	0	0.0019231	0.0001592	637.8403	12.0814238	0.0000000	6
Beagle	SUPER	EAS - SAS	0	0.0003651	0.0001673	637.8403	2.1827753	0.1875155	6
Beagle	SUPER	EUR - SAS	0	-0.0015580	0.0001517	637.8403	-10.2684747	0.0000000	6
Eagle	SUPER	AFR - AMR	0	-0.0010403	0.0001157	637.8403	-8.9920646	0.0000000	6
Eagle	SUPER	AFR - EAS	0	-0.0025019	0.0001434	637.8403	-17.4437864	0.0000000	6
Eagle	SUPER	AFR - EUR	0	-0.0007401	0.0001250	637.8403	-5.9219707	0.0000001	6
Eagle	SUPER	AFR - SAS	0	-0.0020271	0.0001351	637.8403	-15.0030516	0.0000000	6
Eagle	SUPER	AMR - EAS	0	-0.0014616	0.0001520	637.8403	-9.6152489	0.0000000	6
Eagle	SUPER	AMR - EUR	0	0.0003003	0.0001347	637.8403	2.2287756	0.1703975	6
Eagle	SUPER	AMR - SAS	0	-0.0009867	0.0001442	637.8403	-6.8435322	0.0000000	6
Eagle	SUPER	EAS - EUR	0	0.0017619	0.0001592	637.8403	11.0684612	0.0000000	6
Eagle	SUPER	EAS - SAS	0	0.0004748	0.0001673	637.8403	2.8389530	0.0375143	6
Eagle	SUPER	EUR - SAS	0	-0.0012870	0.0001517	637.8403	-8.4824239	0.0000000	6
SHAPEIT	SUPER	AFR - AMR	0	-0.0006899	0.0001157	637.8403	-5.9633534	0.0000000	6
SHAPEIT	SUPER	AFR - EAS	0	-0.0022925	0.0001434	637.8403	-15.9836923	0.0000000	6
SHAPEIT	SUPER	AFR - EUR	0	-0.0002138	0.0001250	637.8403	-1.7110384	0.4278191	6
SHAPEIT	SUPER	AFR - SAS	0	-0.0019980	0.0001351	637.8403	-14.7874880	0.0000000	6
SHAPEIT	SUPER	AMR - EAS	0	-0.0016026	0.0001520	637.8403	-10.5427738	0.0000000	6
SHAPEIT	SUPER	AMR - EUR	0	0.0004761	0.0001347	637.8403	3.5338250	0.0040039	6
SHAPEIT	SUPER	AMR - SAS	0	-0.0013080	0.0001442	637.8403	-9.0717867	0.0000000	6
SHAPEIT	SUPER	EAS - EUR	0	0.0020787	0.0001592	637.8403	13.0587868	0.0000000	6
SHAPEIT	SUPER	EAS - SAS	0	0.0002946	0.0001673	637.8403	1.7610282	0.3974503	6
SHAPEIT	SUPER	EUR - SAS	0	-0.0017841	0.0001517	637.8403	-11.7587502	0.0000000	6
Beagle	SUPER	AFR - AMR	0	-0.0007361	0.0001246	645.0304	-5.9092743	0.0000001	7
Beagle	SUPER	AFR - EAS	0	-0.0025845	0.0001544	645.0304	-16.7364847	0.0000000	7
Beagle	SUPER	AFR - EUR	0	-0.0003421	0.0001345	645.0304	-2.5422493	0.0827634	7
Beagle	SUPER	AFR - SAS	0	-0.0020941	0.0001455	645.0304	-14.3958150	0.0000000	7
Beagle	SUPER	AMR - EAS	0	-0.0018484	0.0001637	645.0304	-11.2942408	0.0000000	7
Beagle	SUPER	AMR - EUR	0	0.0003940	0.0001451	645.0304	2.7163864	0.0526590	7
Beagle	SUPER	AMR - SAS	0	-0.0013580	0.0001552	645.0304	-8.7481578	0.0000000	7
Beagle	SUPER	EAS - EUR	0	0.0022424	0.0001714	645.0304	13.0845182	0.0000000	7
Beagle	SUPER	EAS - SAS	0	0.0004903	0.0001801	645.0304	2.7229525	0.0517329	7
Beagle	SUPER	EUR - SAS	0	-0.0017521	0.0001634	645.0304	-10.7253549	0.0000000	7
Eagle	SUPER	AFR - AMR	0	-0.0010483	0.0001246	645.0304	-8.4161640	0.0000000	7
Eagle	SUPER	AFR - EAS	0	-0.0027912	0.0001544	645.0304	-18.0753326	0.0000000	7
Eagle	SUPER	AFR - EUR	0	-0.0007835	0.0001345	645.0304	-5.8230836	0.0000001	7
Eagle	SUPER	AFR - SAS	0	-0.0022046	0.0001455	645.0304	-15.1551609	0.0000000	7
Eagle	SUPER	AMR - EAS	0	-0.0017429	0.0001637	645.0304	-10.6494816	0.0000000	7
Eagle	SUPER	AMR - EUR	0	0.0002649	0.0001451	645.0304	1.8259556	0.3594153	7
Eagle	SUPER	AMR - SAS	0	-0.0011562	0.0001552	645.0304	-7.4481734	0.0000000	7
Eagle	SUPER	EAS - EUR	0	0.0020077	0.0001714	645.0304	11.7151505	0.0000000	7
Eagle	SUPER	EAS - SAS	0	0.0005866	0.0001801	645.0304	3.2576416	0.0103620	7
Eagle	SUPER	EUR - SAS	0	-0.0014211	0.0001634	645.0304	-8.6993220	0.0000000	7
SHAPEIT	SUPER	AFR - AMR	0	-0.0007233	0.0001246	645.0304	-5.8069757	0.0000001	7
SHAPEIT	SUPER	AFR - EAS	0	-0.0025946	0.0001544	645.0304	-16.8023228	0.0000000	7
SHAPEIT	SUPER	AFR - EUR	0	-0.0002229	0.0001345	645.0304	-1.6570107	0.4615261	7
SHAPEIT	SUPER	AFR - SAS	0	-0.0022346	0.0001455	645.0304	-15.3613727	0.0000000	7
SHAPEIT	SUPER	AMR - EAS	0	-0.0018713	0.0001637	645.0304	-11.4342247	0.0000000	7
SHAPEIT	SUPER	AMR - EUR	0	0.0005004	0.0001451	645.0304	3.4496526	0.0053924	7
SHAPEIT	SUPER	AMR - SAS	0	-0.0015112	0.0001552	645.0304	-9.7350310	0.0000000	7
SHAPEIT	SUPER	EAS - EUR	0	0.0023717	0.0001714	645.0304	13.8388298	0.0000000	7
SHAPEIT	SUPER	EAS - SAS	0	0.0003601	0.0001801	645.0304	1.9994366	0.2673763	7
SHAPEIT	SUPER	EUR - SAS	0	-0.0020116	0.0001634	645.0304	-12.3142848	0.0000000	7
Beagle	SUPER	AFR - AMR	0	-0.0009059	0.0001328	652.8377	-6.8225783	0.0000000	8
Beagle	SUPER	AFR - EAS	0	-0.0028274	0.0001646	652.8377	-17.1771221	0.0000000	8
Beagle	SUPER	AFR - EUR	0	-0.0005110	0.0001434	652.8377	-3.5628465	0.0036009	8
Beagle	SUPER	AFR - SAS	0	-0.0021225	0.0001551	652.8377	-13.6883188	0.0000000	8
Beagle	SUPER	AMR - EAS	0	-0.0019215	0.0001744	652.8377	-11.0148751	0.0000000	8
Beagle	SUPER	AMR - EUR	0	0.0003949	0.0001546	652.8377	2.5540025	0.0803515	8
Beagle	SUPER	AMR - SAS	0	-0.0012166	0.0001655	652.8377	-7.3523501	0.0000000	8
Beagle	SUPER	EAS - EUR	0	0.0023164	0.0001827	652.8377	12.6802982	0.0000000	8
Beagle	SUPER	EAS - SAS	0	0.0007049	0.0001920	652.8377	3.6723189	0.0024081	8
Beagle	SUPER	EUR - SAS	0	-0.0016115	0.0001741	652.8377	-9.2547385	0.0000000	8
Eagle	SUPER	AFR - AMR	0	-0.0013962	0.0001328	652.8377	-10.5155964	0.0000000	8
Eagle	SUPER	AFR - EAS	0	-0.0031391	0.0001646	652.8377	-19.0712514	0.0000000	8
Eagle	SUPER	AFR - EUR	0	-0.0010459	0.0001434	652.8377	-7.2926473	0.0000000	8
Eagle	SUPER	AFR - SAS	0	-0.0023648	0.0001551	652.8377	-15.2511374	0.0000000	8
Eagle	SUPER	AMR - EAS	0	-0.0017429	0.0001744	652.8377	-9.9912717	0.0000000	8
Eagle	SUPER	AMR - EUR	0	0.0003503	0.0001546	652.8377	2.2656932	0.1574626	8
Eagle	SUPER	AMR - SAS	0	-0.0009686	0.0001655	652.8377	-5.8535156	0.0000001	8
Eagle	SUPER	EAS - EUR	0	0.0020933	0.0001827	652.8377	11.4587892	0.0000000	8
Eagle	SUPER	EAS - SAS	0	0.0007744	0.0001920	652.8377	4.0341300	0.0005851	8
Eagle	SUPER	EUR - SAS	0	-0.0013189	0.0001741	652.8377	-7.5743995	0.0000000	8
SHAPEIT	SUPER	AFR - AMR	0	-0.0010047	0.0001328	652.8377	-7.5671741	0.0000000	8
SHAPEIT	SUPER	AFR - EAS	0	-0.0027687	0.0001646	652.8377	-16.8206078	0.0000000	8
SHAPEIT	SUPER	AFR - EUR	0	-0.0003785	0.0001434	652.8377	-2.6391939	0.0646155	8
SHAPEIT	SUPER	AFR - SAS	0	-0.0022780	0.0001551	652.8377	-14.6912134	0.0000000	8
SHAPEIT	SUPER	AMR - EAS	0	-0.0017640	0.0001744	652.8377	-10.1117547	0.0000000	8
SHAPEIT	SUPER	AMR - EUR	0	0.0006262	0.0001546	652.8377	4.0501547	0.0005479	8
SHAPEIT	SUPER	AMR - SAS	0	-0.0012732	0.0001655	652.8377	-7.6946586	0.0000000	8
SHAPEIT	SUPER	EAS - EUR	0	0.0023902	0.0001827	652.8377	13.0842075	0.0000000	8
SHAPEIT	SUPER	EAS - SAS	0	0.0004907	0.0001920	652.8377	2.5564680	0.0798559	8
SHAPEIT	SUPER	EUR - SAS	0	-0.0018995	0.0001741	652.8377	-10.9085553	0.0000000	8
Beagle	SUPER	AFR - AMR	0	-0.0005758	0.0001327	646.2063	-4.3390163	0.0001612	9
Beagle	SUPER	AFR - EAS	0	-0.0026399	0.0001645	646.2063	-16.0458333	0.0000000	9
Beagle	SUPER	AFR - EUR	0	-0.0003953	0.0001433	646.2063	-2.7573899	0.0470956	9
Beagle	SUPER	AFR - SAS	0	-0.0020545	0.0001550	646.2063	-13.2567412	0.0000000	9
Beagle	SUPER	AMR - EAS	0	-0.0020640	0.0001744	646.2063	-11.8377240	0.0000000	9
Beagle	SUPER	AMR - EUR	0	0.0001806	0.0001545	646.2063	1.1684006	0.7694431	9
Beagle	SUPER	AMR - SAS	0	-0.0014787	0.0001654	646.2063	-8.9407557	0.0000000	9
Beagle	SUPER	EAS - EUR	0	0.0022446	0.0001826	646.2063	12.2933033	0.0000000	9
Beagle	SUPER	EAS - SAS	0	0.0005853	0.0001919	646.2063	3.0508456	0.0200357	9
Beagle	SUPER	EUR - SAS	0	-0.0016593	0.0001740	646.2063	-9.5338297	0.0000000	9
Eagle	SUPER	AFR - AMR	0	-0.0009903	0.0001327	646.2063	-7.4620550	0.0000000	9
Eagle	SUPER	AFR - EAS	0	-0.0029117	0.0001645	646.2063	-17.6982554	0.0000000	9
Eagle	SUPER	AFR - EUR	0	-0.0008789	0.0001433	646.2063	-6.1310076	0.0000000	9
Eagle	SUPER	AFR - SAS	0	-0.0022293	0.0001550	646.2063	-14.3846208	0.0000000	9
Eagle	SUPER	AMR - EAS	0	-0.0019214	0.0001744	646.2063	-11.0198779	0.0000000	9
Eagle	SUPER	AMR - EUR	0	0.0001114	0.0001545	646.2063	0.7210139	0.9516534	9
Eagle	SUPER	AMR - SAS	0	-0.0012391	0.0001654	646.2063	-7.4917100	0.0000000	9
Eagle	SUPER	EAS - EUR	0	0.0020329	0.0001826	646.2063	11.1336385	0.0000000	9
Eagle	SUPER	EAS - SAS	0	0.0006824	0.0001919	646.2063	3.5567302	0.0036839	9
Eagle	SUPER	EUR - SAS	0	-0.0013505	0.0001740	646.2063	-7.7595503	0.0000000	9
SHAPEIT	SUPER	AFR - AMR	0	-0.0006411	0.0001327	646.2063	-4.8309266	0.0000168	9
SHAPEIT	SUPER	AFR - EAS	0	-0.0026601	0.0001645	646.2063	-16.1688267	0.0000000	9
SHAPEIT	SUPER	AFR - EUR	0	-0.0002189	0.0001433	646.2063	-1.5268710	0.5453062	9
SHAPEIT	SUPER	AFR - SAS	0	-0.0022083	0.0001550	646.2063	-14.2489629	0.0000000	9
SHAPEIT	SUPER	AMR - EAS	0	-0.0020190	0.0001744	646.2063	-11.5793729	0.0000000	9
SHAPEIT	SUPER	AMR - EUR	0	0.0004222	0.0001545	646.2063	2.7322012	0.0504498	9
SHAPEIT	SUPER	AMR - SAS	0	-0.0015672	0.0001654	646.2063	-9.4758191	0.0000000	9
SHAPEIT	SUPER	EAS - EUR	0	0.0024412	0.0001826	646.2063	13.3701893	0.0000000	9
SHAPEIT	SUPER	EAS - SAS	0	0.0004518	0.0001919	646.2063	2.3548023	0.1293093	9
SHAPEIT	SUPER	EUR - SAS	0	-0.0019894	0.0001740	646.2063	-11.4308893	0.0000000	9
Beagle	SUPER	AFR - AMR	0	-0.0006314	0.0001174	652.8895	-5.3760585	0.0000011	10
Beagle	SUPER	AFR - EAS	0	-0.0022866	0.0001456	652.8895	-15.7044124	0.0000000	10
Beagle	SUPER	AFR - EUR	0	-0.0002953	0.0001269	652.8895	-2.3280256	0.1373257	10
Beagle	SUPER	AFR - SAS	0	-0.0019328	0.0001372	652.8895	-14.0921578	0.0000000	10
Beagle	SUPER	AMR - EAS	0	-0.0016552	0.0001543	652.8895	-10.7262582	0.0000000	10
Beagle	SUPER	AMR - EUR	0	0.0003361	0.0001368	652.8895	2.4572029	0.1018566	10
Beagle	SUPER	AMR - SAS	0	-0.0013014	0.0001464	652.8895	-8.8914666	0.0000000	10
Beagle	SUPER	EAS - EUR	0	0.0019912	0.0001616	652.8895	12.3227540	0.0000000	10
Beagle	SUPER	EAS - SAS	0	0.0003537	0.0001698	652.8895	2.0832255	0.2285453	10
Beagle	SUPER	EUR - SAS	0	-0.0016375	0.0001540	652.8895	-10.6313957	0.0000000	10
Eagle	SUPER	AFR - AMR	0	-0.0010254	0.0001174	652.8895	-8.7305803	0.0000000	10
Eagle	SUPER	AFR - EAS	0	-0.0026105	0.0001456	652.8895	-17.9292957	0.0000000	10
Eagle	SUPER	AFR - EUR	0	-0.0007495	0.0001269	652.8895	-5.9076566	0.0000001	10
Eagle	SUPER	AFR - SAS	0	-0.0021702	0.0001372	652.8895	-15.8223888	0.0000000	10
Eagle	SUPER	AMR - EAS	0	-0.0015851	0.0001543	652.8895	-10.2723781	0.0000000	10
Eagle	SUPER	AMR - EUR	0	0.0002759	0.0001368	652.8895	2.0175080	0.2586651	10
Eagle	SUPER	AMR - SAS	0	-0.0011448	0.0001464	652.8895	-7.8211189	0.0000000	10
Eagle	SUPER	EAS - EUR	0	0.0018611	0.0001616	652.8895	11.5171669	0.0000000	10
Eagle	SUPER	EAS - SAS	0	0.0004403	0.0001698	652.8895	2.5934288	0.0727193	10
Eagle	SUPER	EUR - SAS	0	-0.0014207	0.0001540	652.8895	-9.2238204	0.0000000	10
SHAPEIT	SUPER	AFR - AMR	0	-0.0006838	0.0001174	652.8895	-5.8223057	0.0000001	10
SHAPEIT	SUPER	AFR - EAS	0	-0.0023877	0.0001456	652.8895	-16.3989433	0.0000000	10
SHAPEIT	SUPER	AFR - EUR	0	-0.0001801	0.0001269	652.8895	-1.4200295	0.6149264	10
SHAPEIT	SUPER	AFR - SAS	0	-0.0021015	0.0001372	652.8895	-15.3214358	0.0000000	10
SHAPEIT	SUPER	AMR - EAS	0	-0.0017039	0.0001543	652.8895	-11.0419432	0.0000000	10
SHAPEIT	SUPER	AMR - EUR	0	0.0005037	0.0001368	652.8895	3.6826315	0.0023171	10
SHAPEIT	SUPER	AMR - SAS	0	-0.0014176	0.0001464	652.8895	-9.6853067	0.0000000	10
SHAPEIT	SUPER	EAS - EUR	0	0.0022075	0.0001616	652.8895	13.6614154	0.0000000	10
SHAPEIT	SUPER	EAS - SAS	0	0.0002862	0.0001698	652.8895	1.6857926	0.4434519	10
SHAPEIT	SUPER	EUR - SAS	0	-0.0019213	0.0001540	652.8895	-12.4739082	0.0000000	10
Beagle	SUPER	AFR - AMR	0	-0.0008881	0.0001337	645.9162	-6.6449083	0.0000000	11
Beagle	SUPER	AFR - EAS	0	-0.0025694	0.0001657	645.9162	-15.5069028	0.0000000	11
Beagle	SUPER	AFR - EUR	0	-0.0004370	0.0001444	645.9162	-3.0272624	0.0215370	11
Beagle	SUPER	AFR - SAS	0	-0.0023209	0.0001561	645.9162	-14.8694553	0.0000000	11
Beagle	SUPER	AMR - EAS	0	-0.0016813	0.0001756	645.9162	-9.5741479	0.0000000	11
Beagle	SUPER	AMR - EUR	0	0.0004511	0.0001556	645.9162	2.8982188	0.0316311	11
Beagle	SUPER	AMR - SAS	0	-0.0014328	0.0001666	645.9162	-8.6017126	0.0000000	11
Beagle	SUPER	EAS - EUR	0	0.0021323	0.0001839	645.9162	11.5958272	0.0000000	11
Beagle	SUPER	EAS - SAS	0	0.0002485	0.0001932	645.9162	1.2859601	0.6999985	11
Beagle	SUPER	EUR - SAS	0	-0.0018839	0.0001753	645.9162	-10.7476491	0.0000000	11
Eagle	SUPER	AFR - AMR	0	-0.0012623	0.0001337	645.9162	-9.4446092	0.0000000	11
Eagle	SUPER	AFR - EAS	0	-0.0028490	0.0001657	645.9162	-17.1943653	0.0000000	11
Eagle	SUPER	AFR - EUR	0	-0.0009377	0.0001444	645.9162	-6.4952428	0.0000000	11
Eagle	SUPER	AFR - SAS	0	-0.0024816	0.0001561	645.9162	-15.8989505	0.0000000	11
Eagle	SUPER	AMR - EAS	0	-0.0015867	0.0001756	645.9162	-9.0354637	0.0000000	11
Eagle	SUPER	AMR - EUR	0	0.0003246	0.0001556	645.9162	2.0856446	0.2274959	11
Eagle	SUPER	AMR - SAS	0	-0.0012193	0.0001666	645.9162	-7.3199222	0.0000000	11
Eagle	SUPER	EAS - EUR	0	0.0019113	0.0001839	645.9162	10.3936527	0.0000000	11
Eagle	SUPER	EAS - SAS	0	0.0003674	0.0001932	645.9162	1.9013670	0.3175734	11
Eagle	SUPER	EUR - SAS	0	-0.0015439	0.0001753	645.9162	-8.8080393	0.0000000	11
SHAPEIT	SUPER	AFR - AMR	0	-0.0009258	0.0001337	645.9162	-6.9266630	0.0000000	11
SHAPEIT	SUPER	AFR - EAS	0	-0.0026906	0.0001657	645.9162	-16.2383552	0.0000000	11
SHAPEIT	SUPER	AFR - EUR	0	-0.0003378	0.0001444	645.9162	-2.3398088	0.1337613	11
SHAPEIT	SUPER	AFR - SAS	0	-0.0024526	0.0001561	645.9162	-15.7131379	0.0000000	11
SHAPEIT	SUPER	AMR - EAS	0	-0.0017648	0.0001756	645.9162	-10.0498693	0.0000000	11
SHAPEIT	SUPER	AMR - EUR	0	0.0005880	0.0001556	645.9162	3.7778259	0.0016169	11
SHAPEIT	SUPER	AMR - SAS	0	-0.0015268	0.0001666	645.9162	-9.1662151	0.0000000	11
SHAPEIT	SUPER	EAS - EUR	0	0.0023528	0.0001839	645.9162	12.7946120	0.0000000	11
SHAPEIT	SUPER	EAS - SAS	0	0.0002380	0.0001932	645.9162	1.2316703	0.7328459	11
SHAPEIT	SUPER	EUR - SAS	0	-0.0021148	0.0001753	645.9162	-12.0651479	0.0000000	11
Beagle	SUPER	AFR - AMR	0	-0.0007627	0.0001348	646.0960	-5.6592590	0.0000002	12
Beagle	SUPER	AFR - EAS	0	-0.0025199	0.0001671	646.0960	-15.0821499	0.0000000	12
Beagle	SUPER	AFR - EUR	0	-0.0004272	0.0001456	646.0960	-2.9342325	0.0284667	12
Beagle	SUPER	AFR - SAS	0	-0.0022723	0.0001574	646.0960	-14.4372952	0.0000000	12
Beagle	SUPER	AMR - EAS	0	-0.0017572	0.0001771	646.0960	-9.9235652	0.0000000	12
Beagle	SUPER	AMR - EUR	0	0.0003356	0.0001569	646.0960	2.1381019	0.2052420	12
Beagle	SUPER	AMR - SAS	0	-0.0015096	0.0001680	646.0960	-8.9876408	0.0000000	12
Beagle	SUPER	EAS - EUR	0	0.0020928	0.0001854	646.0960	11.2861403	0.0000000	12
Beagle	SUPER	EAS - SAS	0	0.0002476	0.0001948	646.0960	1.2708241	0.7092743	12
Beagle	SUPER	EUR - SAS	0	-0.0018452	0.0001768	646.0960	-10.4394404	0.0000000	12
Eagle	SUPER	AFR - AMR	0	-0.0011905	0.0001348	646.0960	-8.8332387	0.0000000	12
Eagle	SUPER	AFR - EAS	0	-0.0028558	0.0001671	646.0960	-17.0923896	0.0000000	12
Eagle	SUPER	AFR - EUR	0	-0.0009131	0.0001456	646.0960	-6.2724569	0.0000000	12
Eagle	SUPER	AFR - SAS	0	-0.0023826	0.0001574	646.0960	-15.1378204	0.0000000	12
Eagle	SUPER	AMR - EAS	0	-0.0016653	0.0001771	646.0960	-9.4045699	0.0000000	12
Eagle	SUPER	AMR - EUR	0	0.0002774	0.0001569	646.0960	1.7672893	0.3936989	12
Eagle	SUPER	AMR - SAS	0	-0.0011921	0.0001680	646.0960	-7.0972617	0.0000000	12
Eagle	SUPER	EAS - EUR	0	0.0019427	0.0001854	646.0960	10.4766736	0.0000000	12
Eagle	SUPER	EAS - SAS	0	0.0004732	0.0001948	646.0960	2.4287585	0.1089874	12
Eagle	SUPER	EUR - SAS	0	-0.0014695	0.0001768	646.0960	-8.3137598	0.0000000	12
SHAPEIT	SUPER	AFR - AMR	0	-0.0008319	0.0001348	646.0960	-6.1723147	0.0000000	12
SHAPEIT	SUPER	AFR - EAS	0	-0.0026273	0.0001671	646.0960	-15.7248272	0.0000000	12
SHAPEIT	SUPER	AFR - EUR	0	-0.0003731	0.0001456	646.0960	-2.5626655	0.0786338	12
SHAPEIT	SUPER	AFR - SAS	0	-0.0025230	0.0001574	646.0960	-16.0301577	0.0000000	12
SHAPEIT	SUPER	AMR - EAS	0	-0.0017954	0.0001771	646.0960	-10.1394739	0.0000000	12
SHAPEIT	SUPER	AMR - EUR	0	0.0004588	0.0001569	646.0960	2.9233301	0.0293942	12
SHAPEIT	SUPER	AMR - SAS	0	-0.0016912	0.0001680	646.0960	-10.0685750	0.0000000	12
SHAPEIT	SUPER	EAS - EUR	0	0.0022543	0.0001854	646.0960	12.1569363	0.0000000	12
SHAPEIT	SUPER	EAS - SAS	0	0.0001043	0.0001948	646.0960	0.5352240	0.9836739	12
SHAPEIT	SUPER	EUR - SAS	0	-0.0021500	0.0001768	646.0960	-12.1638958	0.0000000	12
Beagle	SUPER	AFR - AMR	0	-0.0006153	0.0001289	669.0456	-4.7743042	0.0000218	13
Beagle	SUPER	AFR - EAS	0	-0.0023526	0.0001598	669.0456	-14.7259570	0.0000000	13
Beagle	SUPER	AFR - EUR	0	-0.0004368	0.0001392	669.0456	-3.1382968	0.0152258	13
Beagle	SUPER	AFR - SAS	0	-0.0018945	0.0001505	669.0456	-12.5885369	0.0000000	13
Beagle	SUPER	AMR - EAS	0	-0.0017373	0.0001693	669.0456	-10.2610323	0.0000000	13
Beagle	SUPER	AMR - EUR	0	0.0001784	0.0001501	669.0456	1.1888814	0.7578176	13
Beagle	SUPER	AMR - SAS	0	-0.0012793	0.0001606	669.0456	-7.9653293	0.0000000	13
Beagle	SUPER	EAS - EUR	0	0.0019158	0.0001773	669.0456	10.8049849	0.0000000	13
Beagle	SUPER	EAS - SAS	0	0.0004581	0.0001863	669.0456	2.4588011	0.1014366	13
Beagle	SUPER	EUR - SAS	0	-0.0014577	0.0001690	669.0456	-8.6250750	0.0000000	13
Eagle	SUPER	AFR - AMR	0	-0.0009492	0.0001289	669.0456	-7.3652891	0.0000000	13
Eagle	SUPER	AFR - EAS	0	-0.0027004	0.0001598	669.0456	-16.9026822	0.0000000	13
Eagle	SUPER	AFR - EUR	0	-0.0008758	0.0001392	669.0456	-6.2916039	0.0000000	13
Eagle	SUPER	AFR - SAS	0	-0.0022733	0.0001505	669.0456	-15.1057387	0.0000000	13
Eagle	SUPER	AMR - EAS	0	-0.0017512	0.0001693	669.0456	-10.3428558	0.0000000	13
Eagle	SUPER	AMR - EUR	0	0.0000734	0.0001501	669.0456	0.4889550	0.9883788	13
Eagle	SUPER	AMR - SAS	0	-0.0013242	0.0001606	669.0456	-8.2450884	0.0000000	13
Eagle	SUPER	EAS - EUR	0	0.0018246	0.0001773	669.0456	10.2907058	0.0000000	13
Eagle	SUPER	EAS - SAS	0	0.0004270	0.0001863	669.0456	2.2919966	0.1486828	13
Eagle	SUPER	EUR - SAS	0	-0.0013976	0.0001690	669.0456	-8.2694214	0.0000000	13
SHAPEIT	SUPER	AFR - AMR	0	-0.0006906	0.0001289	669.0456	-5.3591698	0.0000011	13
SHAPEIT	SUPER	AFR - EAS	0	-0.0024239	0.0001598	669.0456	-15.1724421	0.0000000	13
SHAPEIT	SUPER	AFR - EUR	0	-0.0003240	0.0001392	669.0456	-2.3274686	0.1374642	13
SHAPEIT	SUPER	AFR - SAS	0	-0.0021408	0.0001505	669.0456	-14.2250141	0.0000000	13
SHAPEIT	SUPER	AMR - EAS	0	-0.0017333	0.0001693	669.0456	-10.2371656	0.0000000	13
SHAPEIT	SUPER	AMR - EUR	0	0.0003667	0.0001501	669.0456	2.4432167	0.1052775	13
SHAPEIT	SUPER	AMR - SAS	0	-0.0014502	0.0001606	669.0456	-9.0295128	0.0000000	13
SHAPEIT	SUPER	EAS - EUR	0	0.0021000	0.0001773	669.0456	11.8438597	0.0000000	13
SHAPEIT	SUPER	EAS - SAS	0	0.0002831	0.0001863	669.0456	1.5197310	0.5499473	13
SHAPEIT	SUPER	EUR - SAS	0	-0.0018168	0.0001690	669.0456	-10.7501608	0.0000000	13
Beagle	SUPER	AFR - AMR	0	-0.0009420	0.0001331	658.3266	-7.0779502	0.0000000	14
Beagle	SUPER	AFR - EAS	0	-0.0023472	0.0001650	658.3266	-14.2257571	0.0000000	14
Beagle	SUPER	AFR - EUR	0	-0.0003467	0.0001438	658.3266	-2.4118908	0.1133633	14
Beagle	SUPER	AFR - SAS	0	-0.0021230	0.0001554	658.3266	-13.6587651	0.0000000	14
Beagle	SUPER	AMR - EAS	0	-0.0014052	0.0001749	658.3266	-8.0357105	0.0000000	14
Beagle	SUPER	AMR - EUR	0	0.0005953	0.0001550	658.3266	3.8408804	0.0012650	14
Beagle	SUPER	AMR - SAS	0	-0.0011809	0.0001659	658.3266	-7.1197449	0.0000000	14
Beagle	SUPER	EAS - EUR	0	0.0020005	0.0001831	658.3266	10.9245709	0.0000000	14
Beagle	SUPER	EAS - SAS	0	0.0002242	0.0001924	658.3266	1.1653455	0.7711588	14
Beagle	SUPER	EUR - SAS	0	-0.0017762	0.0001745	658.3266	-10.1763917	0.0000000	14
Eagle	SUPER	AFR - AMR	0	-0.0012602	0.0001331	658.3266	-9.4686260	0.0000000	14
Eagle	SUPER	AFR - EAS	0	-0.0027527	0.0001650	658.3266	-16.6832941	0.0000000	14
Eagle	SUPER	AFR - EUR	0	-0.0008655	0.0001438	658.3266	-6.0206863	0.0000000	14
Eagle	SUPER	AFR - SAS	0	-0.0022924	0.0001554	658.3266	-14.7491179	0.0000000	14
Eagle	SUPER	AMR - EAS	0	-0.0014925	0.0001749	658.3266	-8.5349566	0.0000000	14
Eagle	SUPER	AMR - EUR	0	0.0003947	0.0001550	658.3266	2.5464490	0.0818751	14
Eagle	SUPER	AMR - SAS	0	-0.0010322	0.0001659	658.3266	-6.2231854	0.0000000	14
Eagle	SUPER	EAS - EUR	0	0.0018871	0.0001831	658.3266	10.3057198	0.0000000	14
Eagle	SUPER	EAS - SAS	0	0.0004602	0.0001924	658.3266	2.3919441	0.1187438	14
Eagle	SUPER	EUR - SAS	0	-0.0014269	0.0001745	658.3266	-8.1749940	0.0000000	14
SHAPEIT	SUPER	AFR - AMR	0	-0.0009985	0.0001331	658.3266	-7.5024312	0.0000000	14
SHAPEIT	SUPER	AFR - EAS	0	-0.0024804	0.0001650	658.3266	-15.0332256	0.0000000	14
SHAPEIT	SUPER	AFR - EUR	0	-0.0003192	0.0001438	658.3266	-2.2204313	0.1733737	14
SHAPEIT	SUPER	AFR - SAS	0	-0.0023074	0.0001554	658.3266	-14.8453584	0.0000000	14
SHAPEIT	SUPER	AMR - EAS	0	-0.0014819	0.0001749	658.3266	-8.4745259	0.0000000	14
SHAPEIT	SUPER	AMR - EUR	0	0.0006793	0.0001550	658.3266	4.3829860	0.0001325	14
SHAPEIT	SUPER	AMR - SAS	0	-0.0013089	0.0001659	658.3266	-7.8910521	0.0000000	14
SHAPEIT	SUPER	EAS - EUR	0	0.0021612	0.0001831	658.3266	11.8024521	0.0000000	14
SHAPEIT	SUPER	EAS - SAS	0	0.0001730	0.0001924	658.3266	0.8992391	0.8971656	14
SHAPEIT	SUPER	EUR - SAS	0	-0.0019882	0.0001745	658.3266	-11.3907276	0.0000000	14
Beagle	SUPER	AFR - AMR	0	-0.0006261	0.0001426	654.9650	-4.3896754	0.0001287	15
Beagle	SUPER	AFR - EAS	0	-0.0025961	0.0001768	654.9650	-14.6832093	0.0000000	15
Beagle	SUPER	AFR - EUR	0	-0.0005065	0.0001541	654.9650	-3.2879788	0.0093636	15
Beagle	SUPER	AFR - SAS	0	-0.0021253	0.0001666	654.9650	-12.7604077	0.0000000	15
Beagle	SUPER	AMR - EAS	0	-0.0019700	0.0001874	654.9650	-10.5134461	0.0000000	15
Beagle	SUPER	AMR - EUR	0	0.0001195	0.0001661	654.9650	0.7197493	0.9519534	15
Beagle	SUPER	AMR - SAS	0	-0.0014992	0.0001777	654.9650	-8.4350110	0.0000000	15
Beagle	SUPER	EAS - EUR	0	0.0020896	0.0001962	654.9650	10.6489538	0.0000000	15
Beagle	SUPER	EAS - SAS	0	0.0004708	0.0002062	654.9650	2.2833077	0.1515599	15
Beagle	SUPER	EUR - SAS	0	-0.0016188	0.0001870	654.9650	-8.6548396	0.0000000	15
Eagle	SUPER	AFR - AMR	0	-0.0009513	0.0001426	654.9650	-6.6701033	0.0000000	15
Eagle	SUPER	AFR - EAS	0	-0.0028416	0.0001768	654.9650	-16.0718895	0.0000000	15
Eagle	SUPER	AFR - EUR	0	-0.0009448	0.0001541	654.9650	-6.1329436	0.0000000	15
Eagle	SUPER	AFR - SAS	0	-0.0023409	0.0001666	654.9650	-14.0550598	0.0000000	15
Eagle	SUPER	AMR - EAS	0	-0.0018903	0.0001874	654.9650	-10.0880715	0.0000000	15
Eagle	SUPER	AMR - EUR	0	0.0000065	0.0001661	654.9650	0.0391443	0.9999995	15
Eagle	SUPER	AMR - SAS	0	-0.0013896	0.0001777	654.9650	-7.8183562	0.0000000	15
Eagle	SUPER	EAS - EUR	0	0.0018968	0.0001962	654.9650	9.6666823	0.0000000	15
Eagle	SUPER	EAS - SAS	0	0.0005007	0.0002062	654.9650	2.4283110	0.1090845	15
Eagle	SUPER	EUR - SAS	0	-0.0013961	0.0001870	654.9650	-7.4644868	0.0000000	15
SHAPEIT	SUPER	AFR - AMR	0	-0.0007169	0.0001426	654.9650	-5.0267370	0.0000064	15
SHAPEIT	SUPER	AFR - EAS	0	-0.0027182	0.0001768	654.9650	-15.3741071	0.0000000	15
SHAPEIT	SUPER	AFR - EUR	0	-0.0004102	0.0001541	654.9650	-2.6625197	0.0607778	15
SHAPEIT	SUPER	AFR - SAS	0	-0.0023991	0.0001666	654.9650	-14.4043760	0.0000000	15
SHAPEIT	SUPER	AMR - EAS	0	-0.0020013	0.0001874	654.9650	-10.6804703	0.0000000	15
SHAPEIT	SUPER	AMR - EUR	0	0.0003067	0.0001661	654.9650	1.8469658	0.3474785	15
SHAPEIT	SUPER	AMR - SAS	0	-0.0016822	0.0001777	654.9650	-9.4643318	0.0000000	15
SHAPEIT	SUPER	EAS - EUR	0	0.0023081	0.0001962	654.9650	11.7625260	0.0000000	15
SHAPEIT	SUPER	EAS - SAS	0	0.0003191	0.0002062	654.9650	1.5477744	0.5316887	15
SHAPEIT	SUPER	EUR - SAS	0	-0.0019889	0.0001870	654.9650	-10.6339192	0.0000000	15
Beagle	SUPER	AFR - AMR	0	-0.0008256	0.0001565	664.8536	-5.2768148	0.0000018	16
Beagle	SUPER	AFR - EAS	0	-0.0029272	0.0001940	664.8536	-15.0908585	0.0000000	16
Beagle	SUPER	AFR - EUR	0	-0.0003634	0.0001690	664.8536	-2.1499089	0.2004070	16
Beagle	SUPER	AFR - SAS	0	-0.0024435	0.0001827	664.8536	-13.3728041	0.0000000	16
Beagle	SUPER	AMR - EAS	0	-0.0021016	0.0002056	664.8536	-10.2228684	0.0000000	16
Beagle	SUPER	AMR - EUR	0	0.0004623	0.0001822	664.8536	2.5371935	0.0837747	16
Beagle	SUPER	AMR - SAS	0	-0.0016179	0.0001950	664.8536	-8.2970204	0.0000000	16
Beagle	SUPER	EAS - EUR	0	0.0025639	0.0002153	664.8536	11.9097484	0.0000000	16
Beagle	SUPER	EAS - SAS	0	0.0004837	0.0002262	664.8536	2.1381830	0.2051714	16
Beagle	SUPER	EUR - SAS	0	-0.0020802	0.0002052	664.8536	-10.1375261	0.0000000	16
Eagle	SUPER	AFR - AMR	0	-0.0011030	0.0001565	664.8536	-7.0493982	0.0000000	16
Eagle	SUPER	AFR - EAS	0	-0.0030829	0.0001940	664.8536	-15.8933189	0.0000000	16
Eagle	SUPER	AFR - EUR	0	-0.0009101	0.0001690	664.8536	-5.3851443	0.0000010	16
Eagle	SUPER	AFR - SAS	0	-0.0023353	0.0001827	664.8536	-12.7805433	0.0000000	16
Eagle	SUPER	AMR - EAS	0	-0.0019799	0.0002056	664.8536	-9.6308900	0.0000000	16
Eagle	SUPER	AMR - EUR	0	0.0001929	0.0001822	664.8536	1.0584865	0.8276504	16
Eagle	SUPER	AMR - SAS	0	-0.0012323	0.0001950	664.8536	-6.3197060	0.0000000	16
Eagle	SUPER	EAS - EUR	0	0.0021727	0.0002153	664.8536	10.0928679	0.0000000	16
Eagle	SUPER	EAS - SAS	0	0.0007475	0.0002262	664.8536	3.3047323	0.0088475	16
Eagle	SUPER	EUR - SAS	0	-0.0014252	0.0002052	664.8536	-6.9454656	0.0000000	16
SHAPEIT	SUPER	AFR - AMR	0	-0.0009145	0.0001565	664.8536	-5.8446828	0.0000001	16
SHAPEIT	SUPER	AFR - EAS	0	-0.0029446	0.0001940	664.8536	-15.1804752	0.0000000	16
SHAPEIT	SUPER	AFR - EUR	0	-0.0004172	0.0001690	664.8536	-2.4684448	0.0991237	16
SHAPEIT	SUPER	AFR - SAS	0	-0.0025304	0.0001827	664.8536	-13.8481551	0.0000000	16
SHAPEIT	SUPER	AMR - EAS	0	-0.0020301	0.0002056	664.8536	-9.8752113	0.0000000	16
SHAPEIT	SUPER	AMR - EUR	0	0.0004973	0.0001822	664.8536	2.7293778	0.0508084	16
SHAPEIT	SUPER	AMR - SAS	0	-0.0016159	0.0001950	664.8536	-8.2867944	0.0000000	16
SHAPEIT	SUPER	EAS - EUR	0	0.0025274	0.0002153	664.8536	11.7404194	0.0000000	16
SHAPEIT	SUPER	EAS - SAS	0	0.0004142	0.0002262	664.8536	1.8310444	0.3564806	16
SHAPEIT	SUPER	EUR - SAS	0	-0.0021132	0.0002052	664.8536	-10.2984605	0.0000000	16
Beagle	SUPER	AFR - AMR	0	-0.0007964	0.0001560	658.8141	-5.1066707	0.0000043	17
Beagle	SUPER	AFR - EAS	0	-0.0030315	0.0001933	658.8141	-15.6799025	0.0000000	17
Beagle	SUPER	AFR - EUR	0	-0.0004975	0.0001685	658.8141	-2.9532303	0.0268961	17
Beagle	SUPER	AFR - SAS	0	-0.0023810	0.0001821	658.8141	-13.0732794	0.0000000	17
Beagle	SUPER	AMR - EAS	0	-0.0022351	0.0002049	658.8141	-10.9081681	0.0000000	17
Beagle	SUPER	AMR - EUR	0	0.0002989	0.0001816	658.8141	1.6459554	0.4685086	17
Beagle	SUPER	AMR - SAS	0	-0.0015846	0.0001944	658.8141	-8.1528713	0.0000000	17
Beagle	SUPER	EAS - EUR	0	0.0025340	0.0002146	658.8141	11.8098300	0.0000000	17
Beagle	SUPER	EAS - SAS	0	0.0006505	0.0002255	658.8141	2.8852531	0.0328256	17
Beagle	SUPER	EUR - SAS	0	-0.0018835	0.0002045	658.8141	-9.2091583	0.0000000	17
Eagle	SUPER	AFR - AMR	0	-0.0010447	0.0001560	658.8141	-6.6985295	0.0000000	17
Eagle	SUPER	AFR - EAS	0	-0.0031568	0.0001933	658.8141	-16.3280326	0.0000000	17
Eagle	SUPER	AFR - EUR	0	-0.0008668	0.0001685	658.8141	-5.1453290	0.0000035	17
Eagle	SUPER	AFR - SAS	0	-0.0024999	0.0001821	658.8141	-13.7261569	0.0000000	17
Eagle	SUPER	AMR - EAS	0	-0.0021121	0.0002049	658.8141	-10.3081226	0.0000000	17
Eagle	SUPER	AMR - EUR	0	0.0001779	0.0001816	658.8141	0.9796281	0.8644404	17
Eagle	SUPER	AMR - SAS	0	-0.0014552	0.0001944	658.8141	-7.4873441	0.0000000	17
Eagle	SUPER	EAS - EUR	0	0.0022900	0.0002146	658.8141	10.6728420	0.0000000	17
Eagle	SUPER	EAS - SAS	0	0.0006569	0.0002255	658.8141	2.9136444	0.0302238	17
Eagle	SUPER	EUR - SAS	0	-0.0016331	0.0002045	658.8141	-7.9850405	0.0000000	17
SHAPEIT	SUPER	AFR - AMR	0	-0.0007836	0.0001560	658.8141	-5.0243014	0.0000065	17
SHAPEIT	SUPER	AFR - EAS	0	-0.0029472	0.0001933	658.8141	-15.2440201	0.0000000	17
SHAPEIT	SUPER	AFR - EUR	0	-0.0003464	0.0001685	658.8141	-2.0562725	0.2405994	17
SHAPEIT	SUPER	AFR - SAS	0	-0.0025388	0.0001821	658.8141	-13.9395701	0.0000000	17
SHAPEIT	SUPER	AMR - EAS	0	-0.0021637	0.0002049	658.8141	-10.5595790	0.0000000	17
SHAPEIT	SUPER	AMR - EUR	0	0.0004372	0.0001816	658.8141	2.4072057	0.1146088	17
SHAPEIT	SUPER	AMR - SAS	0	-0.0017552	0.0001944	658.8141	-9.0307337	0.0000000	17
SHAPEIT	SUPER	EAS - EUR	0	0.0026008	0.0002146	658.8141	12.1212671	0.0000000	17
SHAPEIT	SUPER	EAS - SAS	0	0.0004085	0.0002255	658.8141	1.8116907	0.3676003	17
SHAPEIT	SUPER	EUR - SAS	0	-0.0021924	0.0002045	658.8141	-10.7193448	0.0000000	17
Beagle	SUPER	AFR - AMR	0	-0.0009327	0.0001291	664.4911	-7.2225102	0.0000000	18
Beagle	SUPER	AFR - EAS	0	-0.0026788	0.0001601	664.4911	-16.7334623	0.0000000	18
Beagle	SUPER	AFR - EUR	0	-0.0005296	0.0001395	664.4911	-3.7969750	0.0014986	18
Beagle	SUPER	AFR - SAS	0	-0.0021673	0.0001508	664.4911	-14.3715377	0.0000000	18
Beagle	SUPER	AMR - EAS	0	-0.0017462	0.0001697	664.4911	-10.2918582	0.0000000	18
Beagle	SUPER	AMR - EUR	0	0.0004031	0.0001504	664.4911	2.6802679	0.0579732	18
Beagle	SUPER	AMR - SAS	0	-0.0012346	0.0001609	664.4911	-7.6716621	0.0000000	18
Beagle	SUPER	EAS - EUR	0	0.0021492	0.0001777	664.4911	12.0967277	0.0000000	18
Beagle	SUPER	EAS - SAS	0	0.0005115	0.0001867	664.4911	2.7399718	0.0493654	18
Beagle	SUPER	EUR - SAS	0	-0.0016377	0.0001694	664.4911	-9.6702971	0.0000000	18
Eagle	SUPER	AFR - AMR	0	-0.0012486	0.0001291	664.4911	-9.6685518	0.0000000	18
Eagle	SUPER	AFR - EAS	0	-0.0029528	0.0001601	664.4911	-18.4444619	0.0000000	18
Eagle	SUPER	AFR - EUR	0	-0.0009995	0.0001395	664.4911	-7.1653340	0.0000000	18
Eagle	SUPER	AFR - SAS	0	-0.0022907	0.0001508	664.4911	-15.1898541	0.0000000	18
Eagle	SUPER	AMR - EAS	0	-0.0017042	0.0001697	664.4911	-10.0445600	0.0000000	18
Eagle	SUPER	AMR - EUR	0	0.0002491	0.0001504	664.4911	1.6564004	0.4618919	18
Eagle	SUPER	AMR - SAS	0	-0.0010422	0.0001609	664.4911	-6.4757617	0.0000000	18
Eagle	SUPER	EAS - EUR	0	0.0019533	0.0001777	664.4911	10.9939727	0.0000000	18
Eagle	SUPER	EAS - SAS	0	0.0006620	0.0001867	664.4911	3.5461514	0.0038204	18
Eagle	SUPER	EUR - SAS	0	-0.0012913	0.0001694	664.4911	-7.6246878	0.0000000	18
SHAPEIT	SUPER	AFR - AMR	0	-0.0009898	0.0001291	664.4911	-7.6649213	0.0000000	18
SHAPEIT	SUPER	AFR - EAS	0	-0.0026590	0.0001601	664.4911	-16.6092307	0.0000000	18
SHAPEIT	SUPER	AFR - EUR	0	-0.0003802	0.0001395	664.4911	-2.7257526	0.0513110	18
SHAPEIT	SUPER	AFR - SAS	0	-0.0022900	0.0001508	664.4911	-15.1850913	0.0000000	18
SHAPEIT	SUPER	AMR - EAS	0	-0.0016691	0.0001697	664.4911	-9.8379098	0.0000000	18
SHAPEIT	SUPER	AMR - EUR	0	0.0006096	0.0001504	664.4911	4.0538048	0.0005388	18
SHAPEIT	SUPER	AMR - SAS	0	-0.0013002	0.0001609	664.4911	-8.0790205	0.0000000	18
SHAPEIT	SUPER	EAS - EUR	0	0.0022788	0.0001777	664.4911	12.8257903	0.0000000	18
SHAPEIT	SUPER	EAS - SAS	0	0.0003689	0.0001867	664.4911	1.9762561	0.2787537	18
SHAPEIT	SUPER	EUR - SAS	0	-0.0019098	0.0001694	664.4911	-11.2770529	0.0000000	18
Beagle	SUPER	AFR - AMR	0	-0.0007560	0.0001427	670.7882	-5.2963722	0.0000016	19
Beagle	SUPER	AFR - EAS	0	-0.0026431	0.0001770	670.7882	-14.9366944	0.0000000	19
Beagle	SUPER	AFR - EUR	0	-0.0004454	0.0001542	670.7882	-2.8886689	0.0324874	19
Beagle	SUPER	AFR - SAS	0	-0.0020292	0.0001667	670.7882	-12.1733821	0.0000000	19
Beagle	SUPER	AMR - EAS	0	-0.0018871	0.0001875	670.7882	-10.0625194	0.0000000	19
Beagle	SUPER	AMR - EUR	0	0.0003106	0.0001662	670.7882	1.8687427	0.3353092	19
Beagle	SUPER	AMR - SAS	0	-0.0012732	0.0001779	670.7882	-7.1573935	0.0000000	19
Beagle	SUPER	EAS - EUR	0	0.0021978	0.0001964	670.7882	11.1908489	0.0000000	19
Beagle	SUPER	EAS - SAS	0	0.0006139	0.0002064	670.7882	2.9748722	0.0252022	19
Beagle	SUPER	EUR - SAS	0	-0.0015839	0.0001872	670.7882	-8.4609891	0.0000000	19
Eagle	SUPER	AFR - AMR	0	-0.0011415	0.0001427	670.7882	-7.9966881	0.0000000	19
Eagle	SUPER	AFR - EAS	0	-0.0028256	0.0001770	670.7882	-15.9678166	0.0000000	19
Eagle	SUPER	AFR - EUR	0	-0.0008699	0.0001542	670.7882	-5.6419124	0.0000002	19
Eagle	SUPER	AFR - SAS	0	-0.0021593	0.0001667	670.7882	-12.9535031	0.0000000	19
Eagle	SUPER	AMR - EAS	0	-0.0016841	0.0001875	670.7882	-8.9801814	0.0000000	19
Eagle	SUPER	AMR - EUR	0	0.0002716	0.0001662	670.7882	1.6337859	0.4762326	19
Eagle	SUPER	AMR - SAS	0	-0.0010178	0.0001779	670.7882	-5.7216707	0.0000002	19
Eagle	SUPER	EAS - EUR	0	0.0019557	0.0001964	670.7882	9.9584091	0.0000000	19
Eagle	SUPER	EAS - SAS	0	0.0006663	0.0002064	670.7882	3.2288992	0.0113691	19
Eagle	SUPER	EUR - SAS	0	-0.0012894	0.0001872	670.7882	-6.8879997	0.0000000	19
SHAPEIT	SUPER	AFR - AMR	0	-0.0008285	0.0001427	670.7882	-5.8045254	0.0000001	19
SHAPEIT	SUPER	AFR - EAS	0	-0.0027275	0.0001770	670.7882	-15.4133644	0.0000000	19
SHAPEIT	SUPER	AFR - EUR	0	-0.0003478	0.0001542	670.7882	-2.2557195	0.1608399	19
SHAPEIT	SUPER	AFR - SAS	0	-0.0022152	0.0001667	670.7882	-13.2889796	0.0000000	19
SHAPEIT	SUPER	AMR - EAS	0	-0.0018989	0.0001875	670.7882	-10.1255213	0.0000000	19
SHAPEIT	SUPER	AMR - EUR	0	0.0004808	0.0001662	670.7882	2.8922091	0.0321557	19
SHAPEIT	SUPER	AMR - SAS	0	-0.0013867	0.0001779	670.7882	-7.7950342	0.0000000	19
SHAPEIT	SUPER	EAS - EUR	0	0.0023797	0.0001964	670.7882	12.1172717	0.0000000	19
SHAPEIT	SUPER	EAS - SAS	0	0.0005123	0.0002064	670.7882	2.4824504	0.0958170	19
SHAPEIT	SUPER	EUR - SAS	0	-0.0018674	0.0001872	670.7882	-9.9757321	0.0000000	19
Beagle	SUPER	AFR - AMR	0	-0.0010025	0.0001552	658.4350	-6.4607980	0.0000000	20
Beagle	SUPER	AFR - EAS	0	-0.0029490	0.0001924	658.4350	-15.3304764	0.0000000	20
Beagle	SUPER	AFR - EUR	0	-0.0004579	0.0001676	658.4350	-2.7318575	0.0504773	20
Beagle	SUPER	AFR - SAS	0	-0.0023596	0.0001812	658.4350	-13.0215001	0.0000000	20
Beagle	SUPER	AMR - EAS	0	-0.0019465	0.0002039	658.4350	-9.5478089	0.0000000	20
Beagle	SUPER	AMR - EUR	0	0.0005446	0.0001807	658.4350	3.0141238	0.0224018	20
Beagle	SUPER	AMR - SAS	0	-0.0013571	0.0001934	658.4350	-7.0177931	0.0000000	20
Beagle	SUPER	EAS - EUR	0	0.0024911	0.0002135	658.4350	11.6687765	0.0000000	20
Beagle	SUPER	EAS - SAS	0	0.0005894	0.0002243	658.4350	2.6274413	0.0666120	20
Beagle	SUPER	EUR - SAS	0	-0.0019017	0.0002035	658.4350	-9.3453807	0.0000000	20
Eagle	SUPER	AFR - AMR	0	-0.0013225	0.0001552	658.4350	-8.5231533	0.0000000	20
Eagle	SUPER	AFR - EAS	0	-0.0032978	0.0001924	658.4350	-17.1435811	0.0000000	20
Eagle	SUPER	AFR - EUR	0	-0.0010072	0.0001676	658.4350	-6.0094283	0.0000000	20
Eagle	SUPER	AFR - SAS	0	-0.0025136	0.0001812	658.4350	-13.8713466	0.0000000	20
Eagle	SUPER	AMR - EAS	0	-0.0019752	0.0002039	658.4350	-9.6888847	0.0000000	20
Eagle	SUPER	AMR - EUR	0	0.0003153	0.0001807	658.4350	1.7449844	0.4070748	20
Eagle	SUPER	AMR - SAS	0	-0.0011911	0.0001934	658.4350	-6.1593099	0.0000000	20
Eagle	SUPER	EAS - EUR	0	0.0022906	0.0002135	658.4350	10.7292997	0.0000000	20
Eagle	SUPER	EAS - SAS	0	0.0007842	0.0002243	658.4350	3.4957079	0.0045785	20
Eagle	SUPER	EUR - SAS	0	-0.0015064	0.0002035	658.4350	-7.4026250	0.0000000	20
SHAPEIT	SUPER	AFR - AMR	0	-0.0011291	0.0001552	658.4350	-7.2766280	0.0000000	20
SHAPEIT	SUPER	AFR - EAS	0	-0.0031237	0.0001924	658.4350	-16.2387427	0.0000000	20
SHAPEIT	SUPER	AFR - EUR	0	-0.0004334	0.0001676	658.4350	-2.5856776	0.0741610	20
SHAPEIT	SUPER	AFR - SAS	0	-0.0025271	0.0001812	658.4350	-13.9461593	0.0000000	20
SHAPEIT	SUPER	AMR - EAS	0	-0.0019946	0.0002039	658.4350	-9.7838695	0.0000000	20
SHAPEIT	SUPER	AMR - EUR	0	0.0006957	0.0001807	658.4350	3.8502933	0.0012193	20
SHAPEIT	SUPER	AMR - SAS	0	-0.0013981	0.0001934	658.4350	-7.2296315	0.0000000	20
SHAPEIT	SUPER	EAS - EUR	0	0.0026903	0.0002135	658.4350	12.6019331	0.0000000	20
SHAPEIT	SUPER	EAS - SAS	0	0.0005966	0.0002243	658.4350	2.6593599	0.0612799	20
SHAPEIT	SUPER	EUR - SAS	0	-0.0020938	0.0002035	658.4350	-10.2891744	0.0000000	20
Beagle	SUPER	AFR - AMR	0	-0.0005208	0.0001435	692.0974	-3.6295654	0.0028108	21
Beagle	SUPER	AFR - EAS	0	-0.0020027	0.0001779	692.0974	-11.2579978	0.0000000	21
Beagle	SUPER	AFR - EUR	0	-0.0002092	0.0001550	692.0974	-1.3497751	0.6600462	21
Beagle	SUPER	AFR - SAS	0	-0.0016937	0.0001676	692.0974	-10.1071134	0.0000000	21
Beagle	SUPER	AMR - EAS	0	-0.0014819	0.0001885	692.0974	-7.8600821	0.0000000	21
Beagle	SUPER	AMR - EUR	0	0.0003116	0.0001671	692.0974	1.8648221	0.3374491	21
Beagle	SUPER	AMR - SAS	0	-0.0011729	0.0001788	692.0974	-6.5586227	0.0000000	21
Beagle	SUPER	EAS - EUR	0	0.0017935	0.0001974	692.0974	9.0843246	0.0000000	21
Beagle	SUPER	EAS - SAS	0	0.0003090	0.0002074	692.0974	1.4894484	0.5697001	21
Beagle	SUPER	EUR - SAS	0	-0.0014845	0.0001882	692.0974	-7.8885002	0.0000000	21
Eagle	SUPER	AFR - AMR	0	-0.0009006	0.0001435	692.0974	-6.2764647	0.0000000	21
Eagle	SUPER	AFR - EAS	0	-0.0021879	0.0001779	692.0974	-12.2993288	0.0000000	21
Eagle	SUPER	AFR - EUR	0	-0.0005696	0.0001550	692.0974	-3.6751158	0.0023733	21
Eagle	SUPER	AFR - SAS	0	-0.0018760	0.0001676	692.0974	-11.1950386	0.0000000	21
Eagle	SUPER	AMR - EAS	0	-0.0012873	0.0001885	692.0974	-6.8280330	0.0000000	21
Eagle	SUPER	AMR - EUR	0	0.0003310	0.0001671	692.0974	1.9809010	0.2763978	21
Eagle	SUPER	AMR - SAS	0	-0.0009754	0.0001788	692.0974	-5.4541934	0.0000007	21
Eagle	SUPER	EAS - EUR	0	0.0016183	0.0001974	692.0974	8.1970237	0.0000000	21
Eagle	SUPER	EAS - SAS	0	0.0003119	0.0002074	692.0974	1.5035868	0.5604695	21
Eagle	SUPER	EUR - SAS	0	-0.0013064	0.0001882	692.0974	-6.9420424	0.0000000	21
SHAPEIT	SUPER	AFR - AMR	0	-0.0005376	0.0001435	692.0974	-3.7467632	0.0018110	21
SHAPEIT	SUPER	AFR - EAS	0	-0.0019671	0.0001779	692.0974	-11.0577831	0.0000000	21
SHAPEIT	SUPER	AFR - EUR	0	-0.0001291	0.0001550	692.0974	-0.8328976	0.9203687	21
SHAPEIT	SUPER	AFR - SAS	0	-0.0018169	0.0001676	692.0974	-10.8421074	0.0000000	21
SHAPEIT	SUPER	AMR - EAS	0	-0.0014294	0.0001885	692.0974	-7.5819655	0.0000000	21
SHAPEIT	SUPER	AMR - EUR	0	0.0004085	0.0001671	692.0974	2.4448991	0.1048151	21
SHAPEIT	SUPER	AMR - SAS	0	-0.0012792	0.0001788	692.0974	-7.1533183	0.0000000	21
SHAPEIT	SUPER	EAS - EUR	0	0.0018380	0.0001974	692.0974	9.3097144	0.0000000	21
SHAPEIT	SUPER	EAS - SAS	0	0.0001502	0.0002074	692.0974	0.7240361	0.9509401	21
SHAPEIT	SUPER	EUR - SAS	0	-0.0016878	0.0001882	692.0974	-8.9687205	0.0000000	21
Beagle	SUPER	AFR - AMR	0	-0.0006224	0.0001654	681.1347	-3.7627727	0.0017057	22
Beagle	SUPER	AFR - EAS	0	-0.0023871	0.0002051	681.1347	-11.6403070	0.0000000	22
Beagle	SUPER	AFR - EUR	0	-0.0001454	0.0001787	681.1347	-0.8136906	0.9264331	22
Beagle	SUPER	AFR - SAS	0	-0.0020017	0.0001932	681.1347	-10.3618521	0.0000000	22
Beagle	SUPER	AMR - EAS	0	-0.0017647	0.0002173	681.1347	-8.1194277	0.0000000	22
Beagle	SUPER	AMR - EUR	0	0.0004771	0.0001926	681.1347	2.4764627	0.0971961	22
Beagle	SUPER	AMR - SAS	0	-0.0013793	0.0002062	681.1347	-6.6904427	0.0000000	22
Beagle	SUPER	EAS - EUR	0	0.0022417	0.0002276	681.1347	9.8496764	0.0000000	22
Beagle	SUPER	EAS - SAS	0	0.0003854	0.0002391	681.1347	1.6115084	0.4904665	22
Beagle	SUPER	EUR - SAS	0	-0.0018563	0.0002169	681.1347	-8.5568803	0.0000000	22
Eagle	SUPER	AFR - AMR	0	-0.0009613	0.0001654	681.1347	-5.8108932	0.0000001	22
Eagle	SUPER	AFR - EAS	0	-0.0026950	0.0002051	681.1347	-13.1415978	0.0000000	22
Eagle	SUPER	AFR - EUR	0	-0.0006037	0.0001787	681.1347	-3.3784911	0.0068813	22
Eagle	SUPER	AFR - SAS	0	-0.0022285	0.0001932	681.1347	-11.5356567	0.0000000	22
Eagle	SUPER	AMR - EAS	0	-0.0017338	0.0002173	681.1347	-7.9771222	0.0000000	22
Eagle	SUPER	AMR - EUR	0	0.0003576	0.0001926	681.1347	1.8562377	0.3422421	22
Eagle	SUPER	AMR - SAS	0	-0.0012672	0.0002062	681.1347	-6.1469507	0.0000000	22
Eagle	SUPER	EAS - EUR	0	0.0020913	0.0002276	681.1347	9.1888256	0.0000000	22
Eagle	SUPER	EAS - SAS	0	0.0004665	0.0002391	681.1347	1.9506974	0.2916399	22
Eagle	SUPER	EUR - SAS	0	-0.0016248	0.0002169	681.1347	-7.4896687	0.0000000	22
SHAPEIT	SUPER	AFR - AMR	0	-0.0006362	0.0001654	681.1347	-3.8456205	0.0012382	22
SHAPEIT	SUPER	AFR - EAS	0	-0.0024011	0.0002051	681.1347	-11.7085075	0.0000000	22
SHAPEIT	SUPER	AFR - EUR	0	-0.0000307	0.0001787	681.1347	-0.1717224	0.9998051	22
SHAPEIT	SUPER	AFR - SAS	0	-0.0022147	0.0001932	681.1347	-11.4640855	0.0000000	22
SHAPEIT	SUPER	AMR - EAS	0	-0.0017650	0.0002173	681.1347	-8.1207219	0.0000000	22
SHAPEIT	SUPER	AMR - EUR	0	0.0006055	0.0001926	681.1347	3.1430717	0.0149867	22
SHAPEIT	SUPER	AMR - SAS	0	-0.0015785	0.0002062	681.1347	-7.6568274	0.0000000	22
SHAPEIT	SUPER	EAS - EUR	0	0.0023704	0.0002276	681.1347	10.4151285	0.0000000	22
SHAPEIT	SUPER	EAS - SAS	0	0.0001864	0.0002391	681.1347	0.7796125	0.9364814	22
SHAPEIT	SUPER	EUR - SAS	0	-0.0021840	0.0002169	681.1347	-10.0671510	0.0000000	22
Beagle	SUPER	AFR - AMR	0	-0.0000929	0.0000362	1191.1198	-2.5662199	0.0773715	23
Beagle	SUPER	AFR - EAS	0	-0.0009474	0.0000362	1191.1198	-26.1746698	0.0000000	23
Beagle	SUPER	AFR - EUR	0	-0.0002343	0.0000362	1191.1198	-6.4729229	0.0000000	23
Beagle	SUPER	AFR - SAS	0	-0.0005822	0.0000362	1191.1198	-16.0858537	0.0000000	23
Beagle	SUPER	AMR - EAS	0	-0.0008545	0.0000362	1191.1198	-23.6084499	0.0000000	23
Beagle	SUPER	AMR - EUR	0	-0.0001414	0.0000362	1191.1198	-3.9067030	0.0009367	23
Beagle	SUPER	AMR - SAS	0	-0.0004893	0.0000362	1191.1198	-13.5196338	0.0000000	23
Beagle	SUPER	EAS - EUR	0	0.0007131	0.0000362	1191.1198	19.7017469	0.0000000	23
Beagle	SUPER	EAS - SAS	0	0.0003652	0.0000362	1191.1198	10.0888161	0.0000000	23
Beagle	SUPER	EUR - SAS	0	-0.0003479	0.0000362	1191.1198	-9.6129308	0.0000000	23
Eagle	SUPER	AFR - AMR	0	-0.0000811	0.0000362	1191.1198	-2.2406667	0.1655198	23
Eagle	SUPER	AFR - EAS	0	-0.0009436	0.0000362	1191.1198	-26.0697877	0.0000000	23
Eagle	SUPER	AFR - EUR	0	-0.0002314	0.0000362	1191.1198	-6.3923197	0.0000000	23
Eagle	SUPER	AFR - SAS	0	-0.0006230	0.0000362	1191.1198	-17.2117010	0.0000000	23
Eagle	SUPER	AMR - EAS	0	-0.0008625	0.0000362	1191.1198	-23.8291210	0.0000000	23
Eagle	SUPER	AMR - EUR	0	-0.0001503	0.0000362	1191.1198	-4.1516530	0.0003406	23
Eagle	SUPER	AMR - SAS	0	-0.0005419	0.0000362	1191.1198	-14.9710343	0.0000000	23
Eagle	SUPER	EAS - EUR	0	0.0007122	0.0000362	1191.1198	19.6774680	0.0000000	23
Eagle	SUPER	EAS - SAS	0	0.0003206	0.0000362	1191.1198	8.8580867	0.0000000	23
Eagle	SUPER	EUR - SAS	0	-0.0003916	0.0000362	1191.1198	-10.8193813	0.0000000	23
SHAPEIT	SUPER	AFR - AMR	0	-0.0000758	0.0000362	1191.1198	-2.0954508	0.2226251	23
SHAPEIT	SUPER	AFR - EAS	0	-0.0009169	0.0000362	1191.1198	-25.3317416	0.0000000	23
SHAPEIT	SUPER	AFR - EUR	0	-0.0002284	0.0000362	1191.1198	-6.3112132	0.0000000	23
SHAPEIT	SUPER	AFR - SAS	0	-0.0006043	0.0000362	1191.1198	-16.6950759	0.0000000	23
SHAPEIT	SUPER	AMR - EAS	0	-0.0008410	0.0000362	1191.1198	-23.2362908	0.0000000	23
SHAPEIT	SUPER	AMR - EUR	0	-0.0001526	0.0000362	1191.1198	-4.2157624	0.0002588	23
SHAPEIT	SUPER	AMR - SAS	0	-0.0005284	0.0000362	1191.1198	-14.5996251	0.0000000	23
SHAPEIT	SUPER	EAS - EUR	0	0.0006885	0.0000362	1191.1198	19.0205284	0.0000000	23
SHAPEIT	SUPER	EAS - SAS	0	0.0003126	0.0000362	1191.1198	8.6366657	0.0000000	23
SHAPEIT	SUPER	EUR - SAS	0	-0.0003758	0.0000362	1191.1198	-10.3838627	0.0000000	23

Total Errors

cross_meth_plot <- function(df, p_title, p_func, pop, chrom=as.character(chrom)) {
  p1 <- p_func(df, "Beagle", "SHAPEIT", pop, chrom = chrom)
  p_legend <- cowplot::get_legend(p1)
  
  p1 <- p1 + guides(colour="none") + ggtitle(p_title, paste0("Chromosome ", chrom))
  
  p2 <- p_func(df, "Beagle", "Eagle", pop, chrom = chrom) +
    guides(colour="none") + ggtitle("", "")
  
  p3 <- p_func(df, "SHAPEIT", "Eagle", pop, chrom = chrom) +
    guides(colour="none") + ggtitle("", "")
  
  return(grid.arrange(p1, p_legend, p2, p3, ncol = 2))
  }

plot_total_errors <- function(df, m1, m2, pop, chrom=as.character(chrom)){
  p <- df %>%
    mutate(Beagle = (n_other_beagle + n_flip_beagle),
         Eagle =  (n_other_eagle + n_flip_eagle),
         SHAPEIT =  (n_other_shapeit + n_flip_shapeit)) %>%
    ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
    geom_point() +
    geom_abline(slope = 1, intercept = 0) +
    ggtitle("Total Errors", paste0("Chromosome ", chrom)) +
    theme_classic() +
    xlab(m1) +
    ylab(m2) +
    labs(color="Population") +
    scale_color_manual(values = cbPalette)
  return(p)
}

plot_total_errors_noth <- function(df, m1, m2, pop, chrom=as.character(chrom)){
  p <- df %>%
    mutate(Beagle = (n_switch_b + n_flip_b),
         Eagle =  (n_switch_e + n_flip_e),
         SHAPEIT =  (n_switch_s + n_flip_s)) %>%
    ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
    geom_point() +
    geom_abline(slope = 1, intercept = 0) +
    ggtitle("Total Errors", paste0("Chromosome ", chrom)) +
    theme_classic() +
    xlab(m1) +
    ylab(m2) +
    labs(color="Population") +
    scale_color_manual(values = cbPalette)
  return(p)
}

table_total_errors <- function(df, pop){
  res <- df %>%
    mutate(Beagle = (n_other_beagle + n_flip_beagle),
         Eagle =  (n_other_eagle + n_flip_eagle),
         SHAPEIT =  (n_other_shapeit + n_flip_shapeit)) %>%
    mutate(b_l_e = factor(Beagle < Eagle),
           b_e_e = factor(Beagle == Eagle),
           b_l_s = factor(Beagle < SHAPEIT),
           e_l_b = factor(Beagle > Eagle),
           e_l_s = factor(Eagle < SHAPEIT),
           s_l_b = factor(SHAPEIT < Beagle),
           s_l_e = factor(SHAPEIT < Eagle)) %>%
    tbl_summary(by = !! sym(pop),  
                include = c(b_l_e, b_e_e, b_l_s, e_l_b, e_l_s, s_l_b, s_l_e))
    
  return(res)
}

table_total_errors_noth <- function(df, pop){
  res <- df %>%
    mutate(Beagle = (n_switch_b + n_flip_b),
         Eagle =  (n_switch_e + n_flip_e),
         SHAPEIT =  (n_switch_s + n_flip_s)) %>%
    mutate(b_l_e = factor(Beagle < Eagle),
           b_e_e = factor(Beagle == Eagle),
           b_l_s = factor(Beagle < SHAPEIT),
           e_l_b = factor(Beagle > Eagle),
           e_l_s = factor(Eagle < SHAPEIT),
           s_l_b = factor(SHAPEIT < Beagle),
           s_l_e = factor(SHAPEIT < Eagle)) %>%
    tbl_summary(by = !! sym(pop),  
                include = c(b_l_e, b_e_e, b_l_s, e_l_b, e_l_s, s_l_b, s_l_e))
    
  return(res)
}

Chromosome 1

chrom <- 1

df_switch_trio_noth <- df_switch_trio_noth %>%
  left_join({df_subj_rel %>% select(SUPER, id2)}, by = c("sample" = "id2"))

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-27-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
17d41d5	Andy Beck	2024-05-22

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-27-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
17d41d5	Andy Beck	2024-05-22

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-27-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
17d41d5	Andy Beck	2024-05-22

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-27-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
cb6aa66	Andy Beck	2024-06-06

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-27-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-27-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-27-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-27-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_total_errors(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	187 (93%)	51 (37%)	14 (19%)	34 (32%)	38 (45%)
TRUE	14 (7.0%)	86 (63%)	58 (81%)	73 (68%)	47 (55%)
b_e_e
FALSE	200 (100%)	136 (99%)	71 (99%)	105 (98%)	84 (99%)
TRUE	1 (0.5%)	1 (0.7%)	1 (1.4%)	2 (1.9%)	1 (1.2%)
b_l_s
FALSE	11 (5.5%)	3 (2.2%)	5 (6.9%)	8 (7.5%)	0 (0%)
TRUE	190 (95%)	134 (98%)	67 (93%)	99 (93%)	85 (100%)
e_l_b
FALSE	15 (7.5%)	87 (64%)	59 (82%)	75 (70%)	48 (56%)
TRUE	186 (93%)	50 (36%)	13 (18%)	32 (30%)	37 (44%)
e_l_s
FALSE	4 (2.0%)	31 (23%)	34 (47%)	31 (29%)	3 (3.5%)
TRUE	197 (98%)	106 (77%)	38 (53%)	76 (71%)	82 (96%)
s_l_b
FALSE	191 (95%)	134 (98%)	67 (93%)	100 (93%)	85 (100%)
TRUE	10 (5.0%)	3 (2.2%)	5 (6.9%)	7 (6.5%)	0 (0%)
s_l_e
FALSE	197 (98%)	108 (79%)	38 (53%)	77 (72%)	82 (96%)
TRUE	4 (2.0%)	29 (21%)	34 (47%)	30 (28%)	3 (3.5%)
1 n (%)

table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	196 (98%)	73 (53%)	25 (35%)	43 (40%)	46 (54%)
TRUE	5 (2.5%)	64 (47%)	47 (65%)	64 (60%)	39 (46%)
b_e_e
FALSE	201 (100%)	137 (100%)	72 (100%)	106 (99%)	85 (100%)
TRUE	0 (0%)	0 (0%)	0 (0%)	1 (0.9%)	0 (0%)
b_l_s
FALSE	9 (4.5%)	8 (5.8%)	6 (8.3%)	19 (18%)	1 (1.2%)
TRUE	192 (96%)	129 (94%)	66 (92%)	88 (82%)	84 (99%)
e_l_b
FALSE	5 (2.5%)	64 (47%)	47 (65%)	65 (61%)	39 (46%)
TRUE	196 (98%)	73 (53%)	25 (35%)	42 (39%)	46 (54%)
e_l_s
FALSE	1 (0.5%)	20 (15%)	19 (26%)	23 (21%)	2 (2.4%)
TRUE	200 (100%)	117 (85%)	53 (74%)	84 (79%)	83 (98%)
s_l_b
FALSE	192 (96%)	130 (95%)	66 (92%)	88 (82%)	84 (99%)
TRUE	9 (4.5%)	7 (5.1%)	6 (8.3%)	19 (18%)	1 (1.2%)
s_l_e
FALSE	200 (100%)	118 (86%)	54 (75%)	85 (79%)	83 (98%)
TRUE	1 (0.5%)	19 (14%)	18 (25%)	22 (21%)	2 (2.4%)
1 n (%)

Chromosome 2

chrom <- 2
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-28-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-28-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-28-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-28-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-28-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-28-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-28-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-28-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_total_errors(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	184 (92%)	63 (46%)	15 (21%)	40 (37%)	42 (49%)
TRUE	17 (8.5%)	74 (54%)	57 (79%)	67 (63%)	43 (51%)
b_e_e
FALSE	201 (100%)	135 (99%)	72 (100%)	105 (98%)	84 (99%)
TRUE	0 (0%)	2 (1.5%)	0 (0%)	2 (1.9%)	1 (1.2%)
b_l_s
FALSE	11 (5.5%)	8 (5.8%)	6 (8.3%)	12 (11%)	2 (2.4%)
TRUE	190 (95%)	129 (94%)	66 (92%)	95 (89%)	83 (98%)
e_l_b
FALSE	17 (8.5%)	76 (55%)	57 (79%)	69 (64%)	44 (52%)
TRUE	184 (92%)	61 (45%)	15 (21%)	38 (36%)	41 (48%)
e_l_s
FALSE	1 (0.5%)	26 (19%)	19 (26%)	27 (25%)	4 (4.7%)
TRUE	200 (100%)	111 (81%)	53 (74%)	80 (75%)	81 (95%)
s_l_b
FALSE	190 (95%)	130 (95%)	66 (92%)	97 (91%)	83 (98%)
TRUE	11 (5.5%)	7 (5.1%)	6 (8.3%)	10 (9.3%)	2 (2.4%)
s_l_e
FALSE	200 (100%)	112 (82%)	53 (74%)	82 (77%)	81 (95%)
TRUE	1 (0.5%)	25 (18%)	19 (26%)	25 (23%)	4 (4.7%)
1 n (%)

table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	186 (93%)	81 (59%)	22 (31%)	60 (56%)	55 (65%)
TRUE	15 (7.5%)	56 (41%)	50 (69%)	47 (44%)	30 (35%)
b_e_e
FALSE	201 (100%)	135 (99%)	70 (97%)	106 (99%)	85 (100%)
TRUE	0 (0%)	2 (1.5%)	2 (2.8%)	1 (0.9%)	0 (0%)
b_l_s
FALSE	10 (5.0%)	6 (4.4%)	1 (1.4%)	6 (5.6%)	1 (1.2%)
TRUE	191 (95%)	131 (96%)	71 (99%)	101 (94%)	84 (99%)
e_l_b
FALSE	15 (7.5%)	58 (42%)	52 (72%)	48 (45%)	30 (35%)
TRUE	186 (93%)	79 (58%)	20 (28%)	59 (55%)	55 (65%)
e_l_s
FALSE	2 (1.0%)	24 (18%)	9 (13%)	11 (10%)	0 (0%)
TRUE	199 (99%)	113 (82%)	63 (88%)	96 (90%)	85 (100%)
s_l_b
FALSE	192 (96%)	131 (96%)	71 (99%)	101 (94%)	84 (99%)
TRUE	9 (4.5%)	6 (4.4%)	1 (1.4%)	6 (5.6%)	1 (1.2%)
s_l_e
FALSE	199 (99%)	113 (82%)	63 (88%)	96 (90%)	85 (100%)
TRUE	2 (1.0%)	24 (18%)	9 (13%)	11 (10%)	0 (0%)
1 n (%)

Chromosome 3

chrom <- 3
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-29-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
17d41d5	Andy Beck	2024-05-22

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-29-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-29-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-29-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-29-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-29-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-29-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-29-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_total_errors(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	187 (93%)	56 (41%)	16 (22%)	34 (32%)	39 (46%)
TRUE	14 (7.0%)	81 (59%)	56 (78%)	73 (68%)	46 (54%)
b_e_e
FALSE	201 (100%)	135 (99%)	72 (100%)	106 (99%)	85 (100%)
TRUE	0 (0%)	2 (1.5%)	0 (0%)	1 (0.9%)	0 (0%)
b_l_s
FALSE	14 (7.0%)	7 (5.1%)	6 (8.3%)	12 (11%)	3 (3.5%)
TRUE	187 (93%)	130 (95%)	66 (92%)	95 (89%)	82 (96%)
e_l_b
FALSE	14 (7.0%)	83 (61%)	56 (78%)	74 (69%)	46 (54%)
TRUE	187 (93%)	54 (39%)	16 (22%)	33 (31%)	39 (46%)
e_l_s
FALSE	1 (0.5%)	30 (22%)	25 (35%)	29 (27%)	9 (11%)
TRUE	200 (100%)	107 (78%)	47 (65%)	78 (73%)	76 (89%)
s_l_b
FALSE	188 (94%)	130 (95%)	66 (92%)	98 (92%)	82 (96%)
TRUE	13 (6.5%)	7 (5.1%)	6 (8.3%)	9 (8.4%)	3 (3.5%)
s_l_e
FALSE	200 (100%)	108 (79%)	48 (67%)	78 (73%)	76 (89%)
TRUE	1 (0.5%)	29 (21%)	24 (33%)	29 (27%)	9 (11%)
1 n (%)

table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	192 (96%)	78 (57%)	24 (33%)	57 (53%)	55 (65%)
TRUE	9 (4.5%)	59 (43%)	48 (67%)	50 (47%)	30 (35%)
b_e_e
FALSE	201 (100%)	135 (99%)	72 (100%)	107 (100%)	84 (99%)
TRUE	0 (0%)	2 (1.5%)	0 (0%)	0 (0%)	1 (1.2%)
b_l_s
FALSE	7 (3.5%)	8 (5.8%)	4 (5.6%)	12 (11%)	0 (0%)
TRUE	194 (97%)	129 (94%)	68 (94%)	95 (89%)	85 (100%)
e_l_b
FALSE	9 (4.5%)	61 (45%)	48 (67%)	50 (47%)	31 (36%)
TRUE	192 (96%)	76 (55%)	24 (33%)	57 (53%)	54 (64%)
e_l_s
FALSE	1 (0.5%)	17 (12%)	20 (28%)	14 (13%)	2 (2.4%)
TRUE	200 (100%)	120 (88%)	52 (72%)	93 (87%)	83 (98%)
s_l_b
FALSE	194 (97%)	130 (95%)	68 (94%)	98 (92%)	85 (100%)
TRUE	7 (3.5%)	7 (5.1%)	4 (5.6%)	9 (8.4%)	0 (0%)
s_l_e
FALSE	200 (100%)	121 (88%)	54 (75%)	93 (87%)	83 (98%)
TRUE	1 (0.5%)	16 (12%)	18 (25%)	14 (13%)	2 (2.4%)
1 n (%)

Chromosome 4

chrom <- 4
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-30-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13
17d41d5	Andy Beck	2024-05-22

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-30-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-30-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-30-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-30-5.png

Version	Author	Date
9548985	theandyb	2025-07-14
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-30-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-30-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-30-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_total_errors(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	178 (89%)	56 (41%)	12 (17%)	29 (27%)	37 (44%)
TRUE	23 (11%)	81 (59%)	60 (83%)	78 (73%)	48 (56%)
b_e_e
FALSE	200 (100%)	136 (99%)	72 (100%)	107 (100%)	85 (100%)
TRUE	1 (0.5%)	1 (0.7%)	0 (0%)	0 (0%)	0 (0%)
b_l_s
FALSE	16 (8.0%)	6 (4.4%)	1 (1.4%)	14 (13%)	3 (3.5%)
TRUE	185 (92%)	131 (96%)	71 (99%)	93 (87%)	82 (96%)
e_l_b
FALSE	24 (12%)	82 (60%)	60 (83%)	78 (73%)	48 (56%)
TRUE	177 (88%)	55 (40%)	12 (17%)	29 (27%)	37 (44%)
e_l_s
FALSE	9 (4.5%)	28 (20%)	35 (49%)	30 (28%)	4 (4.7%)
TRUE	192 (96%)	109 (80%)	37 (51%)	77 (72%)	81 (95%)
s_l_b
FALSE	186 (93%)	131 (96%)	71 (99%)	93 (87%)	82 (96%)
TRUE	15 (7.5%)	6 (4.4%)	1 (1.4%)	14 (13%)	3 (3.5%)
s_l_e
FALSE	192 (96%)	110 (80%)	37 (51%)	77 (72%)	81 (95%)
TRUE	9 (4.5%)	27 (20%)	35 (49%)	30 (28%)	4 (4.7%)
1 n (%)

table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	188 (94%)	68 (50%)	13 (18%)	47 (44%)	55 (65%)
TRUE	13 (6.5%)	69 (50%)	59 (82%)	60 (56%)	30 (35%)
b_e_e
FALSE	200 (100%)	136 (99%)	72 (100%)	105 (98%)	82 (96%)
TRUE	1 (0.5%)	1 (0.7%)	0 (0%)	2 (1.9%)	3 (3.5%)
b_l_s
FALSE	21 (10%)	12 (8.8%)	2 (2.8%)	9 (8.4%)	3 (3.5%)
TRUE	180 (90%)	125 (91%)	70 (97%)	98 (92%)	82 (96%)
e_l_b
FALSE	14 (7.0%)	70 (51%)	59 (82%)	62 (58%)	33 (39%)
TRUE	187 (93%)	67 (49%)	13 (18%)	45 (42%)	52 (61%)
e_l_s
FALSE	3 (1.5%)	24 (18%)	20 (28%)	13 (12%)	5 (5.9%)
TRUE	198 (99%)	113 (82%)	52 (72%)	94 (88%)	80 (94%)
s_l_b
FALSE	180 (90%)	125 (91%)	70 (97%)	98 (92%)	82 (96%)
TRUE	21 (10%)	12 (8.8%)	2 (2.8%)	9 (8.4%)	3 (3.5%)
s_l_e
FALSE	198 (99%)	114 (83%)	53 (74%)	94 (88%)	80 (94%)
TRUE	3 (1.5%)	23 (17%)	19 (26%)	13 (12%)	5 (5.9%)
1 n (%)

Chromosome 5

chrom <- 5
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-31-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13
17d41d5	Andy Beck	2024-05-22

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-31-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-31-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-31-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-31-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-31-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-31-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-31-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_total_errors(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	186 (93%)	61 (45%)	14 (19%)	46 (43%)	47 (55%)
TRUE	15 (7.5%)	76 (55%)	58 (81%)	61 (57%)	38 (45%)
b_e_e
FALSE	200 (100%)	137 (100%)	71 (99%)	106 (99%)	82 (96%)
TRUE	1 (0.5%)	0 (0%)	1 (1.4%)	1 (0.9%)	3 (3.5%)
b_l_s
FALSE	7 (3.5%)	8 (5.8%)	5 (6.9%)	12 (11%)	2 (2.4%)
TRUE	194 (97%)	129 (94%)	67 (93%)	95 (89%)	83 (98%)
e_l_b
FALSE	16 (8.0%)	76 (55%)	59 (82%)	62 (58%)	41 (48%)
TRUE	185 (92%)	61 (45%)	13 (18%)	45 (42%)	44 (52%)
e_l_s
FALSE	1 (0.5%)	20 (15%)	27 (38%)	27 (25%)	5 (5.9%)
TRUE	200 (100%)	117 (85%)	45 (63%)	80 (75%)	80 (94%)
s_l_b
FALSE	194 (97%)	130 (95%)	67 (93%)	96 (90%)	83 (98%)
TRUE	7 (3.5%)	7 (5.1%)	5 (6.9%)	11 (10%)	2 (2.4%)
s_l_e
FALSE	200 (100%)	117 (85%)	47 (65%)	81 (76%)	80 (94%)
TRUE	1 (0.5%)	20 (15%)	25 (35%)	26 (24%)	5 (5.9%)
1 n (%)

table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	189 (94%)	76 (55%)	23 (32%)	57 (53%)	53 (62%)
TRUE	12 (6.0%)	61 (45%)	49 (68%)	50 (47%)	32 (38%)
b_e_e
FALSE	201 (100%)	134 (98%)	72 (100%)	105 (98%)	85 (100%)
TRUE	0 (0%)	3 (2.2%)	0 (0%)	2 (1.9%)	0 (0%)
b_l_s
FALSE	17 (8.5%)	7 (5.1%)	2 (2.8%)	12 (11%)	2 (2.4%)
TRUE	184 (92%)	130 (95%)	70 (97%)	95 (89%)	83 (98%)
e_l_b
FALSE	12 (6.0%)	64 (47%)	49 (68%)	52 (49%)	32 (38%)
TRUE	189 (94%)	73 (53%)	23 (32%)	55 (51%)	53 (62%)
e_l_s
FALSE	4 (2.0%)	20 (15%)	12 (17%)	22 (21%)	1 (1.2%)
TRUE	197 (98%)	117 (85%)	60 (83%)	85 (79%)	84 (99%)
s_l_b
FALSE	185 (92%)	130 (95%)	70 (97%)	95 (89%)	84 (99%)
TRUE	16 (8.0%)	7 (5.1%)	2 (2.8%)	12 (11%)	1 (1.2%)
s_l_e
FALSE	197 (98%)	118 (86%)	60 (83%)	86 (80%)	84 (99%)
TRUE	4 (2.0%)	19 (14%)	12 (17%)	21 (20%)	1 (1.2%)
1 n (%)

Chromosome 6

chrom <- 6
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-32-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13
17d41d5	Andy Beck	2024-05-22

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-32-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-32-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-32-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-32-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-32-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-32-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-32-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_total_errors(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	169 (84%)	55 (40%)	12 (17%)	41 (38%)	39 (46%)
TRUE	32 (16%)	82 (60%)	60 (83%)	66 (62%)	46 (54%)
b_e_e
FALSE	200 (100%)	134 (98%)	72 (100%)	107 (100%)	85 (100%)
TRUE	1 (0.5%)	3 (2.2%)	0 (0%)	0 (0%)	0 (0%)
b_l_s
FALSE	6 (3.0%)	13 (9.5%)	3 (4.2%)	12 (11%)	3 (3.5%)
TRUE	195 (97%)	124 (91%)	69 (96%)	95 (89%)	82 (96%)
e_l_b
FALSE	33 (16%)	85 (62%)	60 (83%)	66 (62%)	46 (54%)
TRUE	168 (84%)	52 (38%)	12 (17%)	41 (38%)	39 (46%)
e_l_s
FALSE	6 (3.0%)	34 (25%)	32 (44%)	27 (25%)	7 (8.2%)
TRUE	195 (97%)	103 (75%)	40 (56%)	80 (75%)	78 (92%)
s_l_b
FALSE	195 (97%)	124 (91%)	69 (96%)	96 (90%)	83 (98%)
TRUE	6 (3.0%)	13 (9.5%)	3 (4.2%)	11 (10%)	2 (2.4%)
s_l_e
FALSE	195 (97%)	104 (76%)	42 (58%)	83 (78%)	78 (92%)
TRUE	6 (3.0%)	33 (24%)	30 (42%)	24 (22%)	7 (8.2%)
1 n (%)

table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	185 (92%)	74 (54%)	18 (25%)	53 (50%)	49 (58%)
TRUE	16 (8.0%)	63 (46%)	54 (75%)	54 (50%)	36 (42%)
b_e_e
FALSE	201 (100%)	134 (98%)	71 (99%)	105 (98%)	84 (99%)
TRUE	0 (0%)	3 (2.2%)	1 (1.4%)	2 (1.9%)	1 (1.2%)
b_l_s
FALSE	12 (6.0%)	9 (6.6%)	5 (6.9%)	13 (12%)	4 (4.7%)
TRUE	189 (94%)	128 (93%)	67 (93%)	94 (88%)	81 (95%)
e_l_b
FALSE	16 (8.0%)	66 (48%)	55 (76%)	56 (52%)	37 (44%)
TRUE	185 (92%)	71 (52%)	17 (24%)	51 (48%)	48 (56%)
e_l_s
FALSE	3 (1.5%)	28 (20%)	22 (31%)	20 (19%)	3 (3.5%)
TRUE	198 (99%)	109 (80%)	50 (69%)	87 (81%)	82 (96%)
s_l_b
FALSE	190 (95%)	128 (93%)	67 (93%)	95 (89%)	82 (96%)
TRUE	11 (5.5%)	9 (6.6%)	5 (6.9%)	12 (11%)	3 (3.5%)
s_l_e
FALSE	198 (99%)	110 (80%)	52 (72%)	90 (84%)	83 (98%)
TRUE	3 (1.5%)	27 (20%)	20 (28%)	17 (16%)	2 (2.4%)
1 n (%)

Chromosome 7

chrom <- 7
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-33-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13
17d41d5	Andy Beck	2024-05-22

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-33-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-33-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-33-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-33-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-33-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-33-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-33-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_total_errors(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	172 (86%)	51 (37%)	13 (18%)	33 (31%)	35 (41%)
TRUE	29 (14%)	86 (63%)	59 (82%)	74 (69%)	50 (59%)
b_e_e
FALSE	198 (99%)	137 (100%)	72 (100%)	104 (97%)	85 (100%)
TRUE	3 (1.5%)	0 (0%)	0 (0%)	3 (2.8%)	0 (0%)
b_l_s
FALSE	27 (13%)	2 (1.5%)	4 (5.6%)	20 (19%)	2 (2.4%)
TRUE	174 (87%)	135 (99%)	68 (94%)	87 (81%)	83 (98%)
e_l_b
FALSE	32 (16%)	86 (63%)	59 (82%)	77 (72%)	50 (59%)
TRUE	169 (84%)	51 (37%)	13 (18%)	30 (28%)	35 (41%)
e_l_s
FALSE	5 (2.5%)	30 (22%)	31 (43%)	43 (40%)	11 (13%)
TRUE	196 (98%)	107 (78%)	41 (57%)	64 (60%)	74 (87%)
s_l_b
FALSE	176 (88%)	135 (99%)	68 (94%)	87 (81%)	83 (98%)
TRUE	25 (12%)	2 (1.5%)	4 (5.6%)	20 (19%)	2 (2.4%)
s_l_e
FALSE	196 (98%)	108 (79%)	43 (60%)	64 (60%)	74 (87%)
TRUE	5 (2.5%)	29 (21%)	29 (40%)	43 (40%)	11 (13%)
1 n (%)

table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	177 (88%)	75 (55%)	28 (39%)	44 (41%)	53 (62%)
TRUE	24 (12%)	62 (45%)	44 (61%)	63 (59%)	32 (38%)
b_e_e
FALSE	199 (99%)	135 (99%)	72 (100%)	107 (100%)	83 (98%)
TRUE	2 (1.0%)	2 (1.5%)	0 (0%)	0 (0%)	2 (2.4%)
b_l_s
FALSE	23 (11%)	11 (8.0%)	6 (8.3%)	19 (18%)	2 (2.4%)
TRUE	178 (89%)	126 (92%)	66 (92%)	88 (82%)	83 (98%)
e_l_b
FALSE	26 (13%)	64 (47%)	44 (61%)	63 (59%)	34 (40%)
TRUE	175 (87%)	73 (53%)	28 (39%)	44 (41%)	51 (60%)
e_l_s
FALSE	2 (1.0%)	26 (19%)	17 (24%)	26 (24%)	3 (3.5%)
TRUE	199 (99%)	111 (81%)	55 (76%)	81 (76%)	82 (96%)
s_l_b
FALSE	178 (89%)	126 (92%)	66 (92%)	89 (83%)	83 (98%)
TRUE	23 (11%)	11 (8.0%)	6 (8.3%)	18 (17%)	2 (2.4%)
s_l_e
FALSE	199 (99%)	112 (82%)	55 (76%)	82 (77%)	82 (96%)
TRUE	2 (1.0%)	25 (18%)	17 (24%)	25 (23%)	3 (3.5%)
1 n (%)

Chromosome 8

chrom <- 8
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-34-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13
17d41d5	Andy Beck	2024-05-22

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-34-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-34-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-34-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-34-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-34-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-34-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-34-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_total_errors(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	47 (23%)	9 (6.6%)	1 (1.4%)	2 (1.9%)	5 (5.9%)
TRUE	154 (77%)	128 (93%)	71 (99%)	105 (98%)	80 (94%)
b_e_e
FALSE	200 (100%)	136 (99%)	72 (100%)	107 (100%)	85 (100%)
TRUE	1 (0.5%)	1 (0.7%)	0 (0%)	0 (0%)	0 (0%)
b_l_s
FALSE	133 (66%)	79 (58%)	60 (83%)	67 (63%)	50 (59%)
TRUE	68 (34%)	58 (42%)	12 (17%)	40 (37%)	35 (41%)
e_l_b
FALSE	155 (77%)	129 (94%)	71 (99%)	105 (98%)	80 (94%)
TRUE	46 (23%)	8 (5.8%)	1 (1.4%)	2 (1.9%)	5 (5.9%)
e_l_s
FALSE	144 (72%)	110 (80%)	71 (99%)	88 (82%)	56 (66%)
TRUE	57 (28%)	27 (20%)	1 (1.4%)	19 (18%)	29 (34%)
s_l_b
FALSE	71 (35%)	62 (45%)	14 (19%)	43 (40%)	36 (42%)
TRUE	130 (65%)	75 (55%)	58 (81%)	64 (60%)	49 (58%)
s_l_e
FALSE	58 (29%)	27 (20%)	1 (1.4%)	19 (18%)	29 (34%)
TRUE	143 (71%)	110 (80%)	71 (99%)	88 (82%)	56 (66%)
1 n (%)

table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	187 (93%)	68 (50%)	28 (39%)	58 (54%)	53 (62%)
TRUE	14 (7.0%)	69 (50%)	44 (61%)	49 (46%)	32 (38%)
b_e_e
FALSE	201 (100%)	135 (99%)	70 (97%)	107 (100%)	84 (99%)
TRUE	0 (0%)	2 (1.5%)	2 (2.8%)	0 (0%)	1 (1.2%)
b_l_s
FALSE	16 (8.0%)	11 (8.0%)	16 (22%)	15 (14%)	6 (7.1%)
TRUE	185 (92%)	126 (92%)	56 (78%)	92 (86%)	79 (93%)
e_l_b
FALSE	14 (7.0%)	71 (52%)	46 (64%)	49 (46%)	33 (39%)
TRUE	187 (93%)	66 (48%)	26 (36%)	58 (54%)	52 (61%)
e_l_s
FALSE	1 (0.5%)	20 (15%)	23 (32%)	25 (23%)	4 (4.7%)
TRUE	200 (100%)	117 (85%)	49 (68%)	82 (77%)	81 (95%)
s_l_b
FALSE	187 (93%)	126 (92%)	56 (78%)	92 (86%)	80 (94%)
TRUE	14 (7.0%)	11 (8.0%)	16 (22%)	15 (14%)	5 (5.9%)
s_l_e
FALSE	200 (100%)	118 (86%)	51 (71%)	82 (77%)	81 (95%)
TRUE	1 (0.5%)	19 (14%)	21 (29%)	25 (23%)	4 (4.7%)
1 n (%)

Chromosome 9

chrom <- 9
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-35-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13
9a4bd3e	Andy Beck	2024-05-29
8041a90	Andy Beck	2024-05-29

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-35-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-35-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-35-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-35-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-35-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-35-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-35-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_total_errors(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	166 (83%)	58 (42%)	13 (18%)	39 (36%)	48 (56%)
TRUE	35 (17%)	79 (58%)	59 (82%)	68 (64%)	37 (44%)
b_e_e
FALSE	200 (100%)	137 (100%)	72 (100%)	104 (97%)	85 (100%)
TRUE	1 (0.5%)	0 (0%)	0 (0%)	3 (2.8%)	0 (0%)
b_l_s
FALSE	33 (16%)	16 (12%)	9 (13%)	23 (21%)	8 (9.4%)
TRUE	168 (84%)	121 (88%)	63 (88%)	84 (79%)	77 (91%)
e_l_b
FALSE	36 (18%)	79 (58%)	59 (82%)	71 (66%)	37 (44%)
TRUE	165 (82%)	58 (42%)	13 (18%)	36 (34%)	48 (56%)
e_l_s
FALSE	14 (7.0%)	30 (22%)	32 (44%)	43 (40%)	9 (11%)
TRUE	187 (93%)	107 (78%)	40 (56%)	64 (60%)	76 (89%)
s_l_b
FALSE	170 (85%)	121 (88%)	63 (88%)	85 (79%)	78 (92%)
TRUE	31 (15%)	16 (12%)	9 (13%)	22 (21%)	7 (8.2%)
s_l_e
FALSE	188 (94%)	107 (78%)	41 (57%)	67 (63%)	77 (91%)
TRUE	13 (6.5%)	30 (22%)	31 (43%)	40 (37%)	8 (9.4%)
1 n (%)

table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	181 (90%)	73 (53%)	18 (25%)	51 (48%)	53 (62%)
TRUE	20 (10.0%)	64 (47%)	54 (75%)	56 (52%)	32 (38%)
b_e_e
FALSE	200 (100%)	136 (99%)	72 (100%)	105 (98%)	85 (100%)
TRUE	1 (0.5%)	1 (0.7%)	0 (0%)	2 (1.9%)	0 (0%)
b_l_s
FALSE	29 (14%)	10 (7.3%)	8 (11%)	18 (17%)	8 (9.4%)
TRUE	172 (86%)	127 (93%)	64 (89%)	89 (83%)	77 (91%)
e_l_b
FALSE	21 (10%)	65 (47%)	54 (75%)	58 (54%)	32 (38%)
TRUE	180 (90%)	72 (53%)	18 (25%)	49 (46%)	53 (62%)
e_l_s
FALSE	6 (3.0%)	19 (14%)	22 (31%)	36 (34%)	2 (2.4%)
TRUE	195 (97%)	118 (86%)	50 (69%)	71 (66%)	83 (98%)
s_l_b
FALSE	174 (87%)	127 (93%)	65 (90%)	89 (83%)	79 (93%)
TRUE	27 (13%)	10 (7.3%)	7 (9.7%)	18 (17%)	6 (7.1%)
s_l_e
FALSE	195 (97%)	118 (86%)	50 (69%)	72 (67%)	83 (98%)
TRUE	6 (3.0%)	19 (14%)	22 (31%)	35 (33%)	2 (2.4%)
1 n (%)

Chromosome 10

chrom <- 10
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-36-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
9a4bd3e	Andy Beck	2024-05-29
d6dca59	Andy Beck	2024-05-29
8041a90	Andy Beck	2024-05-29

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-36-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-36-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-36-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-36-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-36-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-36-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-36-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_total_errors(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	162 (81%)	43 (31%)	12 (17%)	37 (35%)	29 (34%)
TRUE	39 (19%)	94 (69%)	60 (83%)	70 (65%)	56 (66%)
b_e_e
FALSE	196 (98%)	135 (99%)	70 (97%)	106 (99%)	85 (100%)
TRUE	5 (2.5%)	2 (1.5%)	2 (2.8%)	1 (0.9%)	0 (0%)
b_l_s
FALSE	19 (9.5%)	12 (8.8%)	10 (14%)	23 (21%)	3 (3.5%)
TRUE	182 (91%)	125 (91%)	62 (86%)	84 (79%)	82 (96%)
e_l_b
FALSE	44 (22%)	96 (70%)	62 (86%)	71 (66%)	56 (66%)
TRUE	157 (78%)	41 (30%)	10 (14%)	36 (34%)	29 (34%)
e_l_s
FALSE	8 (4.0%)	43 (31%)	32 (44%)	40 (37%)	14 (16%)
TRUE	193 (96%)	94 (69%)	40 (56%)	67 (63%)	71 (84%)
s_l_b
FALSE	182 (91%)	128 (93%)	62 (86%)	86 (80%)	82 (96%)
TRUE	19 (9.5%)	9 (6.6%)	10 (14%)	21 (20%)	3 (3.5%)
s_l_e
FALSE	193 (96%)	94 (69%)	41 (57%)	70 (65%)	71 (84%)
TRUE	8 (4.0%)	43 (31%)	31 (43%)	37 (35%)	14 (16%)
1 n (%)

table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	183 (91%)	68 (50%)	21 (29%)	43 (40%)	39 (46%)
TRUE	18 (9.0%)	69 (50%)	51 (71%)	64 (60%)	46 (54%)
b_e_e
FALSE	199 (99%)	137 (100%)	71 (99%)	107 (100%)	83 (98%)
TRUE	2 (1.0%)	0 (0%)	1 (1.4%)	0 (0%)	2 (2.4%)
b_l_s
FALSE	19 (9.5%)	17 (12%)	4 (5.6%)	18 (17%)	5 (5.9%)
TRUE	182 (91%)	120 (88%)	68 (94%)	89 (83%)	80 (94%)
e_l_b
FALSE	20 (10.0%)	69 (50%)	52 (72%)	64 (60%)	48 (56%)
TRUE	181 (90%)	68 (50%)	20 (28%)	43 (40%)	37 (44%)
e_l_s
FALSE	2 (1.0%)	26 (19%)	25 (35%)	28 (26%)	9 (11%)
TRUE	199 (99%)	111 (81%)	47 (65%)	79 (74%)	76 (89%)
s_l_b
FALSE	182 (91%)	123 (90%)	68 (94%)	89 (83%)	80 (94%)
TRUE	19 (9.5%)	14 (10%)	4 (5.6%)	18 (17%)	5 (5.9%)
s_l_e
FALSE	199 (99%)	111 (81%)	48 (67%)	79 (74%)	76 (89%)
TRUE	2 (1.0%)	26 (19%)	24 (33%)	28 (26%)	9 (11%)
1 n (%)

Chromosome 11

chrom <- 10
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-37-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13
ec0ba0b	Andy Beck	2024-05-29
9a4bd3e	Andy Beck	2024-05-29
34c040a	Andy Beck	2024-05-29
d6dca59	Andy Beck	2024-05-29
8041a90	Andy Beck	2024-05-29

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-37-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13
ec0ba0b	Andy Beck	2024-05-29
9a4bd3e	Andy Beck	2024-05-29

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-37-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-37-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-37-5.png

Version	Author	Date
9548985	theandyb	2025-07-14
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-37-6.png

Version	Author	Date
9548985	theandyb	2025-07-14
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-37-7.png

Version	Author	Date
9548985	theandyb	2025-07-14
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-37-8.png

Version	Author	Date
9548985	theandyb	2025-07-14
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

table_total_errors(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	162 (81%)	43 (31%)	12 (17%)	37 (35%)	29 (34%)
TRUE	39 (19%)	94 (69%)	60 (83%)	70 (65%)	56 (66%)
b_e_e
FALSE	196 (98%)	135 (99%)	70 (97%)	106 (99%)	85 (100%)
TRUE	5 (2.5%)	2 (1.5%)	2 (2.8%)	1 (0.9%)	0 (0%)
b_l_s
FALSE	19 (9.5%)	12 (8.8%)	10 (14%)	23 (21%)	3 (3.5%)
TRUE	182 (91%)	125 (91%)	62 (86%)	84 (79%)	82 (96%)
e_l_b
FALSE	44 (22%)	96 (70%)	62 (86%)	71 (66%)	56 (66%)
TRUE	157 (78%)	41 (30%)	10 (14%)	36 (34%)	29 (34%)
e_l_s
FALSE	8 (4.0%)	43 (31%)	32 (44%)	40 (37%)	14 (16%)
TRUE	193 (96%)	94 (69%)	40 (56%)	67 (63%)	71 (84%)
s_l_b
FALSE	182 (91%)	128 (93%)	62 (86%)	86 (80%)	82 (96%)
TRUE	19 (9.5%)	9 (6.6%)	10 (14%)	21 (20%)	3 (3.5%)
s_l_e
FALSE	193 (96%)	94 (69%)	41 (57%)	70 (65%)	71 (84%)
TRUE	8 (4.0%)	43 (31%)	31 (43%)	37 (35%)	14 (16%)
1 n (%)

table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	183 (91%)	68 (50%)	21 (29%)	43 (40%)	39 (46%)
TRUE	18 (9.0%)	69 (50%)	51 (71%)	64 (60%)	46 (54%)
b_e_e
FALSE	199 (99%)	137 (100%)	71 (99%)	107 (100%)	83 (98%)
TRUE	2 (1.0%)	0 (0%)	1 (1.4%)	0 (0%)	2 (2.4%)
b_l_s
FALSE	19 (9.5%)	17 (12%)	4 (5.6%)	18 (17%)	5 (5.9%)
TRUE	182 (91%)	120 (88%)	68 (94%)	89 (83%)	80 (94%)
e_l_b
FALSE	20 (10.0%)	69 (50%)	52 (72%)	64 (60%)	48 (56%)
TRUE	181 (90%)	68 (50%)	20 (28%)	43 (40%)	37 (44%)
e_l_s
FALSE	2 (1.0%)	26 (19%)	25 (35%)	28 (26%)	9 (11%)
TRUE	199 (99%)	111 (81%)	47 (65%)	79 (74%)	76 (89%)
s_l_b
FALSE	182 (91%)	123 (90%)	68 (94%)	89 (83%)	80 (94%)
TRUE	19 (9.5%)	14 (10%)	4 (5.6%)	18 (17%)	5 (5.9%)
s_l_e
FALSE	199 (99%)	111 (81%)	48 (67%)	79 (74%)	76 (89%)
TRUE	2 (1.0%)	26 (19%)	24 (33%)	28 (26%)	9 (11%)
1 n (%)

Chromosome 12

chrom <- 12
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-38-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
76e67f9	Andy Beck	2024-06-26
292c663	Andy Beck	2024-06-13
ec0ba0b	Andy Beck	2024-05-29
9a4bd3e	Andy Beck	2024-05-29
d6dca59	Andy Beck	2024-05-29
8041a90	Andy Beck	2024-05-29

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-38-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
1243aea	Andy Beck	2024-07-03
76e67f9	Andy Beck	2024-06-26
292c663	Andy Beck	2024-06-13
ec0ba0b	Andy Beck	2024-05-29
9a4bd3e	Andy Beck	2024-05-29

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-38-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-38-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-38-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-38-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-38-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-38-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_total_errors(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	179 (89%)	52 (38%)	12 (17%)	38 (36%)	43 (51%)
TRUE	22 (11%)	85 (62%)	60 (83%)	69 (64%)	42 (49%)
b_e_e
FALSE	200 (100%)	135 (99%)	71 (99%)	105 (98%)	85 (100%)
TRUE	1 (0.5%)	2 (1.5%)	1 (1.4%)	2 (1.9%)	0 (0%)
b_l_s
FALSE	29 (14%)	10 (7.3%)	9 (13%)	13 (12%)	5 (5.9%)
TRUE	172 (86%)	127 (93%)	63 (88%)	94 (88%)	80 (94%)
e_l_b
FALSE	23 (11%)	87 (64%)	61 (85%)	71 (66%)	42 (49%)
TRUE	178 (89%)	50 (36%)	11 (15%)	36 (34%)	43 (51%)
e_l_s
FALSE	8 (4.0%)	30 (22%)	27 (38%)	35 (33%)	9 (11%)
TRUE	193 (96%)	107 (78%)	45 (63%)	72 (67%)	76 (89%)
s_l_b
FALSE	174 (87%)	128 (93%)	63 (88%)	95 (89%)	80 (94%)
TRUE	27 (13%)	9 (6.6%)	9 (13%)	12 (11%)	5 (5.9%)
s_l_e
FALSE	194 (97%)	108 (79%)	47 (65%)	72 (67%)	77 (91%)
TRUE	7 (3.5%)	29 (21%)	25 (35%)	35 (33%)	8 (9.4%)
1 n (%)

table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	190 (95%)	65 (47%)	23 (32%)	53 (50%)	59 (69%)
TRUE	11 (5.5%)	72 (53%)	49 (68%)	54 (50%)	26 (31%)
b_e_e
FALSE	201 (100%)	134 (98%)	71 (99%)	102 (95%)	85 (100%)
TRUE	0 (0%)	3 (2.2%)	1 (1.4%)	5 (4.7%)	0 (0%)
b_l_s
FALSE	15 (7.5%)	10 (7.3%)	8 (11%)	10 (9.3%)	5 (5.9%)
TRUE	186 (93%)	127 (93%)	64 (89%)	97 (91%)	80 (94%)
e_l_b
FALSE	11 (5.5%)	75 (55%)	50 (69%)	59 (55%)	26 (31%)
TRUE	190 (95%)	62 (45%)	22 (31%)	48 (45%)	59 (69%)
e_l_s
FALSE	1 (0.5%)	19 (14%)	17 (24%)	20 (19%)	3 (3.5%)
TRUE	200 (100%)	118 (86%)	55 (76%)	87 (81%)	82 (96%)
s_l_b
FALSE	189 (94%)	129 (94%)	65 (90%)	98 (92%)	80 (94%)
TRUE	12 (6.0%)	8 (5.8%)	7 (9.7%)	9 (8.4%)	5 (5.9%)
s_l_e
FALSE	200 (100%)	119 (87%)	55 (76%)	87 (81%)	82 (96%)
TRUE	1 (0.5%)	18 (13%)	17 (24%)	20 (19%)	3 (3.5%)
1 n (%)

Chromosome 13

chrom <- 13
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-39-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
76e67f9	Andy Beck	2024-06-26
292c663	Andy Beck	2024-06-13
9a4bd3e	Andy Beck	2024-05-29
34c040a	Andy Beck	2024-05-29
d6dca59	Andy Beck	2024-05-29
8041a90	Andy Beck	2024-05-29

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-39-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18
1243aea	Andy Beck	2024-07-03
76e67f9	Andy Beck	2024-06-26
292c663	Andy Beck	2024-06-13

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-39-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-39-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
fc667bc	theandyb	2025-06-18

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-39-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-39-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-39-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-39-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_total_errors(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	162 (81%)	55 (40%)	12 (17%)	36 (34%)	33 (39%)
TRUE	39 (19%)	82 (60%)	60 (83%)	71 (66%)	52 (61%)
b_e_e
FALSE	200 (100%)	135 (99%)	72 (100%)	107 (100%)	85 (100%)
TRUE	1 (0.5%)	2 (1.5%)	0 (0%)	0 (0%)	0 (0%)
b_l_s
FALSE	24 (12%)	14 (10%)	14 (19%)	25 (23%)	8 (9.4%)
TRUE	177 (88%)	123 (90%)	58 (81%)	82 (77%)	77 (91%)
e_l_b
FALSE	40 (20%)	84 (61%)	60 (83%)	71 (66%)	52 (61%)
TRUE	161 (80%)	53 (39%)	12 (17%)	36 (34%)	33 (39%)
e_l_s
FALSE	8 (4.0%)	38 (28%)	41 (57%)	47 (44%)	15 (18%)
TRUE	193 (96%)	99 (72%)	31 (43%)	60 (56%)	70 (82%)
s_l_b
FALSE	178 (89%)	123 (90%)	59 (82%)	84 (79%)	78 (92%)
TRUE	23 (11%)	14 (10%)	13 (18%)	23 (21%)	7 (8.2%)
s_l_e
FALSE	193 (96%)	100 (73%)	33 (46%)	63 (59%)	72 (85%)
TRUE	8 (4.0%)	37 (27%)	39 (54%)	44 (41%)	13 (15%)
1 n (%)

table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	179 (89%)	80 (58%)	19 (26%)	53 (50%)	41 (48%)
TRUE	22 (11%)	57 (42%)	53 (74%)	54 (50%)	44 (52%)
b_e_e
FALSE	200 (100%)	136 (99%)	71 (99%)	104 (97%)	83 (98%)
TRUE	1 (0.5%)	1 (0.7%)	1 (1.4%)	3 (2.8%)	2 (2.4%)
b_l_s
FALSE	23 (11%)	11 (8.0%)	11 (15%)	20 (19%)	9 (11%)
TRUE	178 (89%)	126 (92%)	61 (85%)	87 (81%)	76 (89%)
e_l_b
FALSE	23 (11%)	58 (42%)	54 (75%)	57 (53%)	46 (54%)
TRUE	178 (89%)	79 (58%)	18 (25%)	50 (47%)	39 (46%)
e_l_s
FALSE	3 (1.5%)	27 (20%)	27 (38%)	27 (25%)	10 (12%)
TRUE	198 (99%)	110 (80%)	45 (63%)	80 (75%)	75 (88%)
s_l_b
FALSE	181 (90%)	128 (93%)	61 (85%)	88 (82%)	76 (89%)
TRUE	20 (10.0%)	9 (6.6%)	11 (15%)	19 (18%)	9 (11%)
s_l_e
FALSE	198 (99%)	112 (82%)	45 (63%)	82 (77%)	76 (89%)
TRUE	3 (1.5%)	25 (18%)	27 (38%)	25 (23%)	9 (11%)
1 n (%)

Chromosome 14

chrom <- 14
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-40-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13
9a4bd3e	Andy Beck	2024-05-29
34c040a	Andy Beck	2024-05-29
d6dca59	Andy Beck	2024-05-29
8041a90	Andy Beck	2024-05-29

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-40-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-40-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-40-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-40-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-40-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-40-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-40-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_total_errors(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	159 (79%)	52 (38%)	11 (15%)	36 (34%)	32 (38%)
TRUE	42 (21%)	85 (62%)	61 (85%)	71 (66%)	53 (62%)
b_e_e
FALSE	200 (100%)	136 (99%)	72 (100%)	103 (96%)	83 (98%)
TRUE	1 (0.5%)	1 (0.7%)	0 (0%)	4 (3.7%)	2 (2.4%)
b_l_s
FALSE	28 (14%)	24 (18%)	9 (13%)	25 (23%)	6 (7.1%)
TRUE	173 (86%)	113 (82%)	63 (88%)	82 (77%)	79 (93%)
e_l_b
FALSE	43 (21%)	86 (63%)	61 (85%)	75 (70%)	55 (65%)
TRUE	158 (79%)	51 (37%)	11 (15%)	32 (30%)	30 (35%)
e_l_s
FALSE	8 (4.0%)	45 (33%)	37 (51%)	42 (39%)	12 (14%)
TRUE	193 (96%)	92 (67%)	35 (49%)	65 (61%)	73 (86%)
s_l_b
FALSE	176 (88%)	114 (83%)	64 (89%)	84 (79%)	80 (94%)
TRUE	25 (12%)	23 (17%)	8 (11%)	23 (21%)	5 (5.9%)
s_l_e
FALSE	193 (96%)	93 (68%)	35 (49%)	67 (63%)	74 (87%)
TRUE	8 (4.0%)	44 (32%)	37 (51%)	40 (37%)	11 (13%)
1 n (%)

table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	165 (82%)	66 (48%)	21 (29%)	41 (38%)	45 (53%)
TRUE	36 (18%)	71 (52%)	51 (71%)	66 (62%)	40 (47%)
b_e_e
FALSE	199 (99%)	131 (96%)	72 (100%)	105 (98%)	85 (100%)
TRUE	2 (1.0%)	6 (4.4%)	0 (0%)	2 (1.9%)	0 (0%)
b_l_s
FALSE	23 (11%)	12 (8.8%)	6 (8.3%)	16 (15%)	3 (3.5%)
TRUE	178 (89%)	125 (91%)	66 (92%)	91 (85%)	82 (96%)
e_l_b
FALSE	38 (19%)	77 (56%)	51 (71%)	68 (64%)	40 (47%)
TRUE	163 (81%)	60 (44%)	21 (29%)	39 (36%)	45 (53%)
e_l_s
FALSE	8 (4.0%)	24 (18%)	29 (40%)	31 (29%)	7 (8.2%)
TRUE	193 (96%)	113 (82%)	43 (60%)	76 (71%)	78 (92%)
s_l_b
FALSE	178 (89%)	126 (92%)	66 (92%)	92 (86%)	82 (96%)
TRUE	23 (11%)	11 (8.0%)	6 (8.3%)	15 (14%)	3 (3.5%)
s_l_e
FALSE	195 (97%)	113 (82%)	44 (61%)	76 (71%)	78 (92%)
TRUE	6 (3.0%)	24 (18%)	28 (39%)	31 (29%)	7 (8.2%)
1 n (%)

Chromosome 15

chrom <- 15
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-41-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13
9a4bd3e	Andy Beck	2024-05-29
34c040a	Andy Beck	2024-05-29
8041a90	Andy Beck	2024-05-29

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-41-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-41-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-41-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-41-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-41-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-41-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-41-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_total_errors(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	140 (70%)	50 (36%)	12 (17%)	35 (33%)	42 (49%)
TRUE	61 (30%)	87 (64%)	60 (83%)	72 (67%)	43 (51%)
b_e_e
FALSE	198 (99%)	137 (100%)	71 (99%)	103 (96%)	83 (98%)
TRUE	3 (1.5%)	0 (0%)	1 (1.4%)	4 (3.7%)	2 (2.4%)
b_l_s
FALSE	27 (13%)	13 (9.5%)	18 (25%)	28 (26%)	8 (9.4%)
TRUE	174 (87%)	124 (91%)	54 (75%)	79 (74%)	77 (91%)
e_l_b
FALSE	64 (32%)	87 (64%)	61 (85%)	76 (71%)	45 (53%)
TRUE	137 (68%)	50 (36%)	11 (15%)	31 (29%)	40 (47%)
e_l_s
FALSE	22 (11%)	36 (26%)	31 (43%)	48 (45%)	17 (20%)
TRUE	179 (89%)	101 (74%)	41 (57%)	59 (55%)	68 (80%)
s_l_b
FALSE	175 (87%)	124 (91%)	56 (78%)	81 (76%)	77 (91%)
TRUE	26 (13%)	13 (9.5%)	16 (22%)	26 (24%)	8 (9.4%)
s_l_e
FALSE	180 (90%)	103 (75%)	42 (58%)	62 (58%)	70 (82%)
TRUE	21 (10%)	34 (25%)	30 (42%)	45 (42%)	15 (18%)
1 n (%)

table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	153 (76%)	68 (50%)	27 (38%)	51 (48%)	32 (38%)
TRUE	48 (24%)	69 (50%)	45 (63%)	56 (52%)	53 (62%)
b_e_e
FALSE	198 (99%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
TRUE	3 (1.5%)	0 (0%)	0 (0%)	0 (0%)	0 (0%)
b_l_s
FALSE	20 (10.0%)	14 (10%)	14 (19%)	26 (24%)	4 (4.7%)
TRUE	181 (90%)	123 (90%)	58 (81%)	81 (76%)	81 (95%)
e_l_b
FALSE	51 (25%)	69 (50%)	45 (63%)	56 (52%)	53 (62%)
TRUE	150 (75%)	68 (50%)	27 (38%)	51 (48%)	32 (38%)
e_l_s
FALSE	14 (7.0%)	28 (20%)	20 (28%)	34 (32%)	12 (14%)
TRUE	187 (93%)	109 (80%)	52 (72%)	73 (68%)	73 (86%)
s_l_b
FALSE	182 (91%)	124 (91%)	59 (82%)	82 (77%)	81 (95%)
TRUE	19 (9.5%)	13 (9.5%)	13 (18%)	25 (23%)	4 (4.7%)
s_l_e
FALSE	188 (94%)	110 (80%)	53 (74%)	74 (69%)	75 (88%)
TRUE	13 (6.5%)	27 (20%)	19 (26%)	33 (31%)	10 (12%)
1 n (%)

Chromosome 16

chrom <- 16
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-42-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13
9a4bd3e	Andy Beck	2024-05-29
d6dca59	Andy Beck	2024-05-29
8041a90	Andy Beck	2024-05-29

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-42-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-42-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-42-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
01d26a4	theandyb	2025-06-18

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-42-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-42-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-42-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-42-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_total_errors(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	146 (73%)	60 (44%)	18 (25%)	24 (22%)	38 (45%)
TRUE	55 (27%)	77 (56%)	54 (75%)	83 (78%)	47 (55%)
b_e_e
FALSE	199 (99%)	136 (99%)	72 (100%)	107 (100%)	81 (95%)
TRUE	2 (1.0%)	1 (0.7%)	0 (0%)	0 (0%)	4 (4.7%)
b_l_s
FALSE	28 (14%)	15 (11%)	10 (14%)	18 (17%)	7 (8.2%)
TRUE	173 (86%)	122 (89%)	62 (86%)	89 (83%)	78 (92%)
e_l_b
FALSE	57 (28%)	78 (57%)	54 (75%)	83 (78%)	51 (60%)
TRUE	144 (72%)	59 (43%)	18 (25%)	24 (22%)	34 (40%)
e_l_s
FALSE	15 (7.5%)	31 (23%)	32 (44%)	45 (42%)	14 (16%)
TRUE	186 (93%)	106 (77%)	40 (56%)	62 (58%)	71 (84%)
s_l_b
FALSE	175 (87%)	122 (89%)	63 (88%)	89 (83%)	78 (92%)
TRUE	26 (13%)	15 (11%)	9 (13%)	18 (17%)	7 (8.2%)
s_l_e
FALSE	187 (93%)	107 (78%)	42 (58%)	63 (59%)	72 (85%)
TRUE	14 (7.0%)	30 (22%)	30 (42%)	44 (41%)	13 (15%)
1 n (%)

table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	155 (77%)	71 (52%)	24 (33%)	41 (38%)	52 (61%)
TRUE	46 (23%)	66 (48%)	48 (67%)	66 (62%)	33 (39%)
b_e_e
FALSE	200 (100%)	136 (99%)	72 (100%)	104 (97%)	85 (100%)
TRUE	1 (0.5%)	1 (0.7%)	0 (0%)	3 (2.8%)	0 (0%)
b_l_s
FALSE	23 (11%)	14 (10%)	13 (18%)	18 (17%)	9 (11%)
TRUE	178 (89%)	123 (90%)	59 (82%)	89 (83%)	76 (89%)
e_l_b
FALSE	47 (23%)	67 (49%)	48 (67%)	69 (64%)	33 (39%)
TRUE	154 (77%)	70 (51%)	24 (33%)	38 (36%)	52 (61%)
e_l_s
FALSE	13 (6.5%)	19 (14%)	25 (35%)	35 (33%)	6 (7.1%)
TRUE	188 (94%)	118 (86%)	47 (65%)	72 (67%)	79 (93%)
s_l_b
FALSE	180 (90%)	124 (91%)	59 (82%)	91 (85%)	77 (91%)
TRUE	21 (10%)	13 (9.5%)	13 (18%)	16 (15%)	8 (9.4%)
s_l_e
FALSE	188 (94%)	122 (89%)	47 (65%)	73 (68%)	79 (93%)
TRUE	13 (6.5%)	15 (11%)	25 (35%)	34 (32%)	6 (7.1%)
1 n (%)

Chromosome 17

chrom <- 17
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-43-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13
9a4bd3e	Andy Beck	2024-05-29
34c040a	Andy Beck	2024-05-29
d6dca59	Andy Beck	2024-05-29
8041a90	Andy Beck	2024-05-29

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-43-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-43-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-43-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-43-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-43-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-43-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-43-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_total_errors(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	151 (75%)	55 (40%)	13 (18%)	35 (33%)	27 (32%)
TRUE	50 (25%)	82 (60%)	59 (82%)	72 (67%)	58 (68%)
b_e_e
FALSE	196 (98%)	133 (97%)	72 (100%)	105 (98%)	83 (98%)
TRUE	5 (2.5%)	4 (2.9%)	0 (0%)	2 (1.9%)	2 (2.4%)
b_l_s
FALSE	35 (17%)	20 (15%)	13 (18%)	28 (26%)	12 (14%)
TRUE	166 (83%)	117 (85%)	59 (82%)	79 (74%)	73 (86%)
e_l_b
FALSE	55 (27%)	86 (63%)	59 (82%)	74 (69%)	60 (71%)
TRUE	146 (73%)	51 (37%)	13 (18%)	33 (31%)	25 (29%)
e_l_s
FALSE	27 (13%)	44 (32%)	42 (58%)	53 (50%)	22 (26%)
TRUE	174 (87%)	93 (68%)	30 (42%)	54 (50%)	63 (74%)
s_l_b
FALSE	168 (84%)	118 (86%)	60 (83%)	80 (75%)	73 (86%)
TRUE	33 (16%)	19 (14%)	12 (17%)	27 (25%)	12 (14%)
s_l_e
FALSE	174 (87%)	95 (69%)	32 (44%)	57 (53%)	63 (74%)
TRUE	27 (13%)	42 (31%)	40 (56%)	50 (47%)	22 (26%)
1 n (%)

table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	146 (73%)	69 (50%)	25 (35%)	43 (40%)	36 (42%)
TRUE	55 (27%)	68 (50%)	47 (65%)	64 (60%)	49 (58%)
b_e_e
FALSE	200 (100%)	136 (99%)	70 (97%)	103 (96%)	84 (99%)
TRUE	1 (0.5%)	1 (0.7%)	2 (2.8%)	4 (3.7%)	1 (1.2%)
b_l_s
FALSE	34 (17%)	18 (13%)	12 (17%)	24 (22%)	14 (16%)
TRUE	167 (83%)	119 (87%)	60 (83%)	83 (78%)	71 (84%)
e_l_b
FALSE	56 (28%)	69 (50%)	49 (68%)	68 (64%)	50 (59%)
TRUE	145 (72%)	68 (50%)	23 (32%)	39 (36%)	35 (41%)
e_l_s
FALSE	12 (6.0%)	31 (23%)	27 (38%)	35 (33%)	21 (25%)
TRUE	189 (94%)	106 (77%)	45 (63%)	72 (67%)	64 (75%)
s_l_b
FALSE	172 (86%)	120 (88%)	61 (85%)	84 (79%)	71 (84%)
TRUE	29 (14%)	17 (12%)	11 (15%)	23 (21%)	14 (16%)
s_l_e
FALSE	189 (94%)	107 (78%)	46 (64%)	74 (69%)	64 (75%)
TRUE	12 (6.0%)	30 (22%)	26 (36%)	33 (31%)	21 (25%)
1 n (%)

Chromosome 18

chrom <- 18
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-44-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13
9a4bd3e	Andy Beck	2024-05-29
d6dca59	Andy Beck	2024-05-29
8041a90	Andy Beck	2024-05-29

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-44-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-44-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-44-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-44-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-44-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-44-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-44-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_total_errors(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	164 (82%)	66 (48%)	17 (24%)	40 (37%)	41 (48%)
TRUE	37 (18%)	71 (52%)	55 (76%)	67 (63%)	44 (52%)
b_e_e
FALSE	197 (98%)	133 (97%)	71 (99%)	104 (97%)	82 (96%)
TRUE	4 (2.0%)	4 (2.9%)	1 (1.4%)	3 (2.8%)	3 (3.5%)
b_l_s
FALSE	28 (14%)	20 (15%)	11 (15%)	32 (30%)	5 (5.9%)
TRUE	173 (86%)	117 (85%)	61 (85%)	75 (70%)	80 (94%)
e_l_b
FALSE	41 (20%)	75 (55%)	56 (78%)	70 (65%)	47 (55%)
TRUE	160 (80%)	62 (45%)	16 (22%)	37 (35%)	38 (45%)
e_l_s
FALSE	11 (5.5%)	25 (18%)	28 (39%)	47 (44%)	18 (21%)
TRUE	190 (95%)	112 (82%)	44 (61%)	60 (56%)	67 (79%)
s_l_b
FALSE	174 (87%)	118 (86%)	64 (89%)	77 (72%)	80 (94%)
TRUE	27 (13%)	19 (14%)	8 (11%)	30 (28%)	5 (5.9%)
s_l_e
FALSE	191 (95%)	115 (84%)	45 (63%)	62 (58%)	67 (79%)
TRUE	10 (5.0%)	22 (16%)	27 (38%)	45 (42%)	18 (21%)
1 n (%)

table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	169 (84%)	85 (62%)	17 (24%)	39 (36%)	45 (53%)
TRUE	32 (16%)	52 (38%)	55 (76%)	68 (64%)	40 (47%)
b_e_e
FALSE	199 (99%)	134 (98%)	71 (99%)	104 (97%)	83 (98%)
TRUE	2 (1.0%)	3 (2.2%)	1 (1.4%)	3 (2.8%)	2 (2.4%)
b_l_s
FALSE	20 (10.0%)	12 (8.8%)	12 (17%)	23 (21%)	7 (8.2%)
TRUE	181 (90%)	125 (91%)	60 (83%)	84 (79%)	78 (92%)
e_l_b
FALSE	34 (17%)	55 (40%)	56 (78%)	71 (66%)	42 (49%)
TRUE	167 (83%)	82 (60%)	16 (22%)	36 (34%)	43 (51%)
e_l_s
FALSE	6 (3.0%)	21 (15%)	27 (38%)	31 (29%)	13 (15%)
TRUE	195 (97%)	116 (85%)	45 (63%)	76 (71%)	72 (85%)
s_l_b
FALSE	183 (91%)	126 (92%)	60 (83%)	87 (81%)	78 (92%)
TRUE	18 (9.0%)	11 (8.0%)	12 (17%)	20 (19%)	7 (8.2%)
s_l_e
FALSE	195 (97%)	116 (85%)	46 (64%)	76 (71%)	72 (85%)
TRUE	6 (3.0%)	21 (15%)	26 (36%)	31 (29%)	13 (15%)
1 n (%)

Chromosome 19

chrom <- 19
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-45-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13
9a4bd3e	Andy Beck	2024-05-29
cd54733	Andy Beck	2024-05-29

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-45-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-45-3.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-45-4.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-45-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-45-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-45-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-45-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_total_errors(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	107 (53%)	44 (32%)	24 (33%)	32 (30%)	36 (42%)
TRUE	94 (47%)	93 (68%)	48 (67%)	75 (70%)	49 (58%)
b_e_e
FALSE	199 (99%)	133 (97%)	71 (99%)	105 (98%)	84 (99%)
TRUE	2 (1.0%)	4 (2.9%)	1 (1.4%)	2 (1.9%)	1 (1.2%)
b_l_s
FALSE	49 (24%)	25 (18%)	21 (29%)	33 (31%)	12 (14%)
TRUE	152 (76%)	112 (82%)	51 (71%)	74 (69%)	73 (86%)
e_l_b
FALSE	96 (48%)	97 (71%)	49 (68%)	77 (72%)	50 (59%)
TRUE	105 (52%)	40 (29%)	23 (32%)	30 (28%)	35 (41%)
e_l_s
FALSE	53 (26%)	54 (39%)	32 (44%)	53 (50%)	24 (28%)
TRUE	148 (74%)	83 (61%)	40 (56%)	54 (50%)	61 (72%)
s_l_b
FALSE	155 (77%)	113 (82%)	52 (72%)	78 (73%)	73 (86%)
TRUE	46 (23%)	24 (18%)	20 (28%)	29 (27%)	12 (14%)
s_l_e
FALSE	151 (75%)	87 (64%)	40 (56%)	55 (51%)	63 (74%)
TRUE	50 (25%)	50 (36%)	32 (44%)	52 (49%)	22 (26%)
1 n (%)

table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	143 (71%)	52 (38%)	31 (43%)	51 (48%)	48 (56%)
TRUE	58 (29%)	85 (62%)	41 (57%)	56 (52%)	37 (44%)
b_e_e
FALSE	199 (99%)	134 (98%)	72 (100%)	106 (99%)	84 (99%)
TRUE	2 (1.0%)	3 (2.2%)	0 (0%)	1 (0.9%)	1 (1.2%)
b_l_s
FALSE	42 (21%)	24 (18%)	20 (28%)	36 (34%)	9 (11%)
TRUE	159 (79%)	113 (82%)	52 (72%)	71 (66%)	76 (89%)
e_l_b
FALSE	60 (30%)	88 (64%)	41 (57%)	57 (53%)	38 (45%)
TRUE	141 (70%)	49 (36%)	31 (43%)	50 (47%)	47 (55%)
e_l_s
FALSE	32 (16%)	41 (30%)	26 (36%)	43 (40%)	6 (7.1%)
TRUE	169 (84%)	96 (70%)	46 (64%)	64 (60%)	79 (93%)
s_l_b
FALSE	161 (80%)	114 (83%)	52 (72%)	76 (71%)	77 (91%)
TRUE	40 (20%)	23 (17%)	20 (28%)	31 (29%)	8 (9.4%)
s_l_e
FALSE	174 (87%)	99 (72%)	46 (64%)	65 (61%)	79 (93%)
TRUE	27 (13%)	38 (28%)	26 (36%)	42 (39%)	6 (7.1%)
1 n (%)

Chromosome 20

chrom <- 20
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-46-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13
9a4bd3e	Andy Beck	2024-05-29
cd54733	Andy Beck	2024-05-29

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-46-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-46-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-46-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-46-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-46-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-46-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-46-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_total_errors(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	141 (70%)	59 (43%)	22 (31%)	34 (32%)	39 (46%)
TRUE	60 (30%)	78 (57%)	50 (69%)	73 (68%)	46 (54%)
b_e_e
FALSE	197 (98%)	136 (99%)	72 (100%)	106 (99%)	83 (98%)
TRUE	4 (2.0%)	1 (0.7%)	0 (0%)	1 (0.9%)	2 (2.4%)
b_l_s
FALSE	57 (28%)	25 (18%)	15 (21%)	21 (20%)	17 (20%)
TRUE	144 (72%)	112 (82%)	57 (79%)	86 (80%)	68 (80%)
e_l_b
FALSE	64 (32%)	79 (58%)	50 (69%)	74 (69%)	48 (56%)
TRUE	137 (68%)	58 (42%)	22 (31%)	33 (31%)	37 (44%)
e_l_s
FALSE	37 (18%)	43 (31%)	31 (43%)	46 (43%)	23 (27%)
TRUE	164 (82%)	94 (69%)	41 (57%)	61 (57%)	62 (73%)
s_l_b
FALSE	148 (74%)	115 (84%)	59 (82%)	88 (82%)	69 (81%)
TRUE	53 (26%)	22 (16%)	13 (18%)	19 (18%)	16 (19%)
s_l_e
FALSE	167 (83%)	97 (71%)	43 (60%)	63 (59%)	62 (73%)
TRUE	34 (17%)	40 (29%)	29 (40%)	44 (41%)	23 (27%)
1 n (%)

table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	151 (75%)	59 (43%)	23 (32%)	37 (35%)	44 (52%)
TRUE	50 (25%)	78 (57%)	49 (68%)	70 (65%)	41 (48%)
b_e_e
FALSE	197 (98%)	134 (98%)	71 (99%)	103 (96%)	85 (100%)
TRUE	4 (2.0%)	3 (2.2%)	1 (1.4%)	4 (3.7%)	0 (0%)
b_l_s
FALSE	49 (24%)	22 (16%)	16 (22%)	31 (29%)	16 (19%)
TRUE	152 (76%)	115 (84%)	56 (78%)	76 (71%)	69 (81%)
e_l_b
FALSE	54 (27%)	81 (59%)	50 (69%)	74 (69%)	41 (48%)
TRUE	147 (73%)	56 (41%)	22 (31%)	33 (31%)	44 (52%)
e_l_s
FALSE	27 (13%)	33 (24%)	27 (38%)	43 (40%)	18 (21%)
TRUE	174 (87%)	104 (76%)	45 (63%)	64 (60%)	67 (79%)
s_l_b
FALSE	154 (77%)	116 (85%)	58 (81%)	77 (72%)	70 (82%)
TRUE	47 (23%)	21 (15%)	14 (19%)	30 (28%)	15 (18%)
s_l_e
FALSE	180 (90%)	105 (77%)	46 (64%)	64 (60%)	68 (80%)
TRUE	21 (10%)	32 (23%)	26 (36%)	43 (40%)	17 (20%)
1 n (%)

Chromosome 21

chrom <- 21
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-47-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13
9a4bd3e	Andy Beck	2024-05-29

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-47-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-47-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-47-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

table_total_errors(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	112 (56%)	44 (32%)	19 (26%)	35 (33%)	33 (39%)
TRUE	89 (44%)	93 (68%)	53 (74%)	72 (67%)	52 (61%)
b_e_e
FALSE	200 (100%)	133 (97%)	71 (99%)	102 (95%)	81 (95%)
TRUE	1 (0.5%)	4 (2.9%)	1 (1.4%)	5 (4.7%)	4 (4.7%)
b_l_s
FALSE	40 (20%)	18 (13%)	22 (31%)	32 (30%)	14 (16%)
TRUE	161 (80%)	119 (87%)	50 (69%)	75 (70%)	71 (84%)
e_l_b
FALSE	90 (45%)	97 (71%)	54 (75%)	77 (72%)	56 (66%)
TRUE	111 (55%)	40 (29%)	18 (25%)	30 (28%)	29 (34%)
e_l_s
FALSE	45 (22%)	56 (41%)	37 (51%)	47 (44%)	27 (32%)
TRUE	156 (78%)	81 (59%)	35 (49%)	60 (56%)	58 (68%)
s_l_b
FALSE	166 (83%)	122 (89%)	51 (71%)	79 (74%)	71 (84%)
TRUE	35 (17%)	15 (11%)	21 (29%)	28 (26%)	14 (16%)
s_l_e
FALSE	158 (79%)	84 (61%)	36 (50%)	61 (57%)	60 (71%)
TRUE	43 (21%)	53 (39%)	36 (50%)	46 (43%)	25 (29%)
1 n (%)

table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	147 (73%)	54 (39%)	26 (36%)	47 (44%)	40 (47%)
TRUE	54 (27%)	83 (61%)	46 (64%)	60 (56%)	45 (53%)
b_e_e
FALSE	196 (98%)	133 (97%)	72 (100%)	103 (96%)	83 (98%)
TRUE	5 (2.5%)	4 (2.9%)	0 (0%)	4 (3.7%)	2 (2.4%)
b_l_s
FALSE	33 (16%)	26 (19%)	19 (26%)	20 (19%)	13 (15%)
TRUE	168 (84%)	111 (81%)	53 (74%)	87 (81%)	72 (85%)
e_l_b
FALSE	59 (29%)	87 (64%)	46 (64%)	64 (60%)	47 (55%)
TRUE	142 (71%)	50 (36%)	26 (36%)	43 (40%)	38 (45%)
e_l_s
FALSE	23 (11%)	41 (30%)	32 (44%)	44 (41%)	20 (24%)
TRUE	178 (89%)	96 (70%)	40 (56%)	63 (59%)	65 (76%)
s_l_b
FALSE	169 (84%)	113 (82%)	53 (74%)	90 (84%)	73 (86%)
TRUE	32 (16%)	24 (18%)	19 (26%)	17 (16%)	12 (14%)
s_l_e
FALSE	180 (90%)	99 (72%)	41 (57%)	68 (64%)	66 (78%)
TRUE	21 (10%)	38 (28%)	31 (43%)	39 (36%)	19 (22%)
1 n (%)

Chromosome 22

chrom <- 22
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-48-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13
9a4bd3e	Andy Beck	2024-05-29

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-48-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-48-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-48-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

table_total_errors(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	113 (56%)	35 (26%)	15 (21%)	33 (31%)	28 (33%)
TRUE	88 (44%)	102 (74%)	57 (79%)	74 (69%)	57 (67%)
b_e_e
FALSE	197 (98%)	136 (99%)	72 (100%)	102 (95%)	84 (99%)
TRUE	4 (2.0%)	1 (0.7%)	0 (0%)	5 (4.7%)	1 (1.2%)
b_l_s
FALSE	62 (31%)	33 (24%)	19 (26%)	33 (31%)	21 (25%)
TRUE	139 (69%)	104 (76%)	53 (74%)	74 (69%)	64 (75%)
e_l_b
FALSE	92 (46%)	103 (75%)	57 (79%)	79 (74%)	58 (68%)
TRUE	109 (54%)	34 (25%)	15 (21%)	28 (26%)	27 (32%)
e_l_s
FALSE	53 (26%)	66 (48%)	48 (67%)	54 (50%)	39 (46%)
TRUE	148 (74%)	71 (52%)	24 (33%)	53 (50%)	46 (54%)
s_l_b
FALSE	143 (71%)	108 (79%)	54 (75%)	76 (71%)	64 (75%)
TRUE	58 (29%)	29 (21%)	18 (25%)	31 (29%)	21 (25%)
s_l_e
FALSE	153 (76%)	74 (54%)	24 (33%)	56 (52%)	46 (54%)
TRUE	48 (24%)	63 (46%)	48 (67%)	51 (48%)	39 (46%)
1 n (%)

table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	118 (59%)	53 (39%)	20 (28%)	48 (45%)	36 (42%)
TRUE	83 (41%)	84 (61%)	52 (72%)	59 (55%)	49 (58%)
b_e_e
FALSE	198 (99%)	136 (99%)	71 (99%)	101 (94%)	82 (96%)
TRUE	3 (1.5%)	1 (0.7%)	1 (1.4%)	6 (5.6%)	3 (3.5%)
b_l_s
FALSE	58 (29%)	29 (21%)	21 (29%)	29 (27%)	12 (14%)
TRUE	143 (71%)	108 (79%)	51 (71%)	78 (73%)	73 (86%)
e_l_b
FALSE	86 (43%)	85 (62%)	53 (74%)	65 (61%)	52 (61%)
TRUE	115 (57%)	52 (38%)	19 (26%)	42 (39%)	33 (39%)
e_l_s
FALSE	61 (30%)	49 (36%)	38 (53%)	49 (46%)	23 (27%)
TRUE	140 (70%)	88 (64%)	34 (47%)	58 (54%)	62 (73%)
s_l_b
FALSE	146 (73%)	110 (80%)	52 (72%)	79 (74%)	74 (87%)
TRUE	55 (27%)	27 (20%)	20 (28%)	28 (26%)	11 (13%)
s_l_e
FALSE	144 (72%)	90 (66%)	34 (47%)	62 (58%)	66 (78%)
TRUE	57 (28%)	47 (34%)	38 (53%)	45 (42%)	19 (22%)
1 n (%)

Chromosome X

plot_total_errors(df_switch_x, "Beagle", "Eagle", "pop", "X")

Past versions of unnamed-chunk-49-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13
9a4bd3e	Andy Beck	2024-05-29

plot_total_errors(df_switch_x, "Beagle", "SHAPEIT", "pop", "X")

Past versions of unnamed-chunk-49-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_errors(df_switch_x, "SHAPEIT", "Eagle", "pop", "X")

Past versions of unnamed-chunk-49-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

table_total_errors(df_switch_x, "pop")

Characteristic	AFR N = 2001	AMR N = 2001	EAS N = 2001	EUR N = 2001	SAS N = 2001
b_l_e
FALSE	1 (0.5%)	6 (3.0%)	1 (0.5%)	0 (0%)	1 (0.5%)
TRUE	199 (100%)	194 (97%)	199 (100%)	200 (100%)	199 (100%)
b_e_e
FALSE	200 (100%)	200 (100%)	200 (100%)	200 (100%)	200 (100%)
b_l_s
FALSE	73 (37%)	63 (32%)	107 (54%)	80 (40%)	97 (49%)
TRUE	127 (64%)	137 (69%)	93 (47%)	120 (60%)	103 (52%)
e_l_b
FALSE	199 (100%)	194 (97%)	199 (100%)	200 (100%)	199 (100%)
TRUE	1 (0.5%)	6 (3.0%)	1 (0.5%)	0 (0%)	1 (0.5%)
e_l_s
FALSE	198 (99%)	188 (94%)	200 (100%)	198 (99%)	198 (99%)
TRUE	2 (1.0%)	12 (6.0%)	0 (0%)	2 (1.0%)	2 (1.0%)
s_l_b
FALSE	135 (68%)	141 (71%)	101 (51%)	127 (64%)	103 (52%)
TRUE	65 (33%)	59 (30%)	99 (50%)	73 (37%)	97 (49%)
s_l_e
FALSE	3 (1.5%)	14 (7.0%)	0 (0%)	2 (1.0%)	2 (1.0%)
TRUE	197 (99%)	186 (93%)	200 (100%)	198 (99%)	198 (99%)
1 n (%)

cross_meth_plot(df_switch_x, "Total Errors", plot_total_errors, "pop", "X")

Past versions of unnamed-chunk-49-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

Error Rate

plot_total_rate <- function(df, m1, m2, pop, chrom=as.character(chrom)){
  p <- df %>%
    mutate(Beagle = (n_other_beagle + n_flip_beagle) / n_hets,
         Eagle = (n_other_eagle + n_flip_eagle) / n_hets,
         SHAPEIT = (n_other_shapeit + n_flip_shapeit) / n_hets) %>%
    ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
    geom_point() +
    geom_abline(slope = 1, intercept = 0) +
    ggtitle("Error Rate", paste0("Chromosome ", chrom)) +
    theme_classic() +
    xlab(m1) +
    ylab(m2) +
    labs(color="Population") +
    scale_color_manual(values = cbPalette)
  return(p)
}

plot_total_rate_noth <- function(df, m1, m2, pop, chrom=as.character(chrom)){
  p <- df %>%
    mutate(Beagle = (n_switch_b + n_flip_b) / n_het,
         Eagle = (n_switch_e + n_flip_e) / n_het,
         SHAPEIT = (n_switch_s + n_flip_s) / n_het) %>%
    ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
    geom_point() +
    geom_abline(slope = 1, intercept = 0) +
    ggtitle("Error Rate", paste0("Chromosome ", chrom)) +
    theme_classic() +
    xlab(m1) +
    ylab(m2) +
    labs(color="Population") +
    scale_color_manual(values = cbPalette)
  return(p)
}

Chromosome 1

chrom <- 1 
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-51-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-51-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-51-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-51-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-51-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-51-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-51-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-51-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 2

chrom <- 2
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-52-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-52-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-52-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-52-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-52-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-52-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-52-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-52-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 3

chrom <- 3
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-53-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03
292c663	Andy Beck	2024-06-13

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-53-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-53-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-53-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-53-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-53-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-53-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-53-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 4

chrom <- 4
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-54-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-54-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-54-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-54-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-54-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-54-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-54-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-54-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 5

chrom <- 5
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-55-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-55-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-55-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-55-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-55-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-55-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-55-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-55-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 6

chrom <- 6
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-56-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-56-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-56-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-56-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-56-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-56-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-56-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-56-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 7

chrom <- 7
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-57-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-57-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-57-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-57-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-57-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-57-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-57-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-57-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 8

chrom <- 8
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-58-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-58-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-58-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-58-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-58-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-58-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-58-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-58-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 9

chrom <- 9
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-59-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-59-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-59-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-59-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-59-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-59-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-59-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-59-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 10

chrom <- 10
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-60-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19
c2bd645	theandyb	2025-06-16
1243aea	Andy Beck	2024-07-03

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-60-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-60-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-60-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-60-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-60-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-60-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-60-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 11

chrom <- 11
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-61-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-61-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-61-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-61-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-61-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-61-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-61-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-61-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 12

chrom <- 12
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-62-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-62-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-62-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-62-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-62-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-62-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-62-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-62-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 13

chrom <- 13
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-63-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-63-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-63-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-63-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-63-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-63-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-63-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-63-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 14

chrom <- 14
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-64-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-64-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-64-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-64-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-64-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-64-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-64-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-64-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 15

chrom <- 15
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-65-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-65-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-65-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-65-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-65-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-65-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-65-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-65-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 16

chrom <- 16
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-66-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-66-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-66-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-66-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-66-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-66-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-66-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-66-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 17

chrom <- 17
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-67-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-67-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-67-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-67-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-67-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-67-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-67-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-67-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 18

chrom <- 18
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-68-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-68-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-68-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-68-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-68-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-68-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-68-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-68-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 19

chrom <- 19
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-69-1.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-69-2.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-69-3.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-69-4.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-69-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-69-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-69-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-69-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 20

chrom <- 20 
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-70-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-70-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-70-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-70-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-70-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-70-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-70-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-70-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 21

chrom <- 21 
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-71-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-71-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-71-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-71-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Chromosome 22

chrom <- 22 
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-72-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-72-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-72-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-72-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

Chromosome X

plot_total_rate(df_switch_x, "Beagle", "Eagle", "pop", "X")

Past versions of unnamed-chunk-73-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_x, "Beagle", "SHAPEIT", "pop", "X")

Past versions of unnamed-chunk-73-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_total_rate(df_switch_x, "SHAPEIT", "Eagle", "pop", "X")

Past versions of unnamed-chunk-73-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

cross_meth_plot(df_switch_x, "Total Errors", plot_total_rate, "pop", "X")

Past versions of unnamed-chunk-73-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

Non-flip Switches

plot_switches <- function(df, m1, m2, pop, chrom=15){
  p <- df %>%
    mutate(Beagle = n_other_beagle,
         Eagle = n_other_eagle,
         SHAPEIT = n_other_shapeit) %>%
    ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
    geom_point() +
    geom_abline(slope = 1, intercept = 0) +
    ggtitle("Switches", paste0("Chromosome ", chrom)) +
    theme_classic() +
    xlab(m1) +
    ylab(m2) +
    labs(color="Population") +
    scale_color_manual(values = cbPalette)
  return(p)
}

plot_switches_noth <- function(df, m1, m2, pop, chrom=15){
  p <- df %>%
    mutate(Beagle = n_switch_b,
         Eagle = n_switch_e,
         SHAPEIT = n_switch_s) %>%
    ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
    geom_point() +
    geom_abline(slope = 1, intercept = 0) +
    ggtitle("Switches", paste0("Chromosome ", chrom)) +
    theme_classic() +
    xlab(m1) +
    ylab(m2) +
    labs(color="Population") +
    scale_color_manual(values = cbPalette)
  return(p)
}

table_switches <- function(df, pop){
  res <- df %>%
    mutate(Beagle = (n_other_beagle ),
         Eagle =  (n_other_eagle),
         SHAPEIT =  (n_other_shapeit)) %>%
    mutate(b_l_e = factor(Beagle < Eagle),
           b_l_s = factor(Beagle < SHAPEIT),
           e_l_b = factor(Beagle > Eagle),
           e_l_s = factor(Eagle < SHAPEIT),
           s_l_b = factor(SHAPEIT < Beagle),
           s_l_e = factor(SHAPEIT < Eagle)) %>%
    tbl_summary(by = !! sym(pop),  
                include = c(b_l_e, b_l_s, e_l_b, e_l_s, s_l_b, s_l_e))
    
  return(res)
}

table_switches_noth <- function(df, pop){
  res <- df %>%
    mutate(Beagle = (n_switch_b ),
         Eagle =  (n_switch_e),
         SHAPEIT =  (n_switch_s)) %>%
    mutate(b_l_e = factor(Beagle < Eagle),
           b_l_s = factor(Beagle < SHAPEIT),
           e_l_b = factor(Beagle > Eagle),
           e_l_s = factor(Eagle < SHAPEIT),
           s_l_b = factor(SHAPEIT < Beagle),
           s_l_e = factor(SHAPEIT < Eagle)) %>%
    tbl_summary(by = !! sym(pop),  
                include = c(b_l_e, b_l_s, e_l_b, e_l_s, s_l_b, s_l_e))
    
  return(res)
}

Chromosome 1

chrom <- 1

plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-75-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-75-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-75-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-75-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-75-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-75-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_switches(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
b_l_s
FALSE	163 (81%)	81 (59%)	39 (54%)	72 (67%)	53 (62%)
TRUE	38 (19%)	56 (41%)	33 (46%)	35 (33%)	32 (38%)
e_l_b
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
e_l_s
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	41 (20%)	58 (42%)	33 (46%)	37 (35%)	33 (39%)
TRUE	160 (80%)	79 (58%)	39 (54%)	70 (65%)	52 (61%)
s_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
1 n (%)

table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	0 (0%)	1 (0.7%)	0 (0%)	0 (0%)	0 (0%)
TRUE	201 (100%)	136 (99%)	72 (100%)	107 (100%)	85 (100%)
b_l_s
FALSE	150 (75%)	78 (57%)	33 (46%)	72 (67%)	44 (52%)
TRUE	51 (25%)	59 (43%)	39 (54%)	35 (33%)	41 (48%)
e_l_b
FALSE	201 (100%)	136 (99%)	72 (100%)	107 (100%)	85 (100%)
TRUE	0 (0%)	1 (0.7%)	0 (0%)	0 (0%)	0 (0%)
e_l_s
FALSE	201 (100%)	136 (99%)	72 (100%)	107 (100%)	85 (100%)
TRUE	0 (0%)	1 (0.7%)	0 (0%)	0 (0%)	0 (0%)
s_l_b
FALSE	54 (27%)	61 (45%)	39 (54%)	39 (36%)	41 (48%)
TRUE	147 (73%)	76 (55%)	33 (46%)	68 (64%)	44 (52%)
s_l_e
FALSE	0 (0%)	1 (0.7%)	0 (0%)	0 (0%)	0 (0%)
TRUE	201 (100%)	136 (99%)	72 (100%)	107 (100%)	85 (100%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-75-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-75-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 2

chrom <- 2
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-76-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-76-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-76-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-76-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-76-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-76-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_switches(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
b_l_s
FALSE	161 (80%)	78 (57%)	31 (43%)	65 (61%)	50 (59%)
TRUE	40 (20%)	59 (43%)	41 (57%)	42 (39%)	35 (41%)
e_l_b
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
e_l_s
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	43 (21%)	62 (45%)	42 (58%)	43 (40%)	35 (41%)
TRUE	158 (79%)	75 (55%)	30 (42%)	64 (60%)	50 (59%)
s_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
1 n (%)

table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
b_l_s
FALSE	131 (65%)	75 (55%)	31 (43%)	70 (65%)	52 (61%)
TRUE	70 (35%)	62 (45%)	41 (57%)	37 (35%)	33 (39%)
e_l_b
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
e_l_s
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	75 (37%)	65 (47%)	41 (57%)	39 (36%)	38 (45%)
TRUE	126 (63%)	72 (53%)	31 (43%)	68 (64%)	47 (55%)
s_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-76-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-76-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 3

chrom <- 3
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-77-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-77-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-77-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-77-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-77-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-77-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_switches(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
b_l_s
FALSE	154 (77%)	75 (55%)	35 (49%)	76 (71%)	41 (48%)
TRUE	47 (23%)	62 (45%)	37 (51%)	31 (29%)	44 (52%)
e_l_b
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
e_l_s
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	48 (24%)	65 (47%)	41 (57%)	34 (32%)	48 (56%)
TRUE	153 (76%)	72 (53%)	31 (43%)	73 (68%)	37 (44%)
s_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
1 n (%)

table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
b_l_s
FALSE	132 (66%)	68 (50%)	30 (42%)	61 (57%)	38 (45%)
TRUE	69 (34%)	69 (50%)	42 (58%)	46 (43%)	47 (55%)
e_l_b
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
e_l_s
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	75 (37%)	72 (53%)	42 (58%)	49 (46%)	51 (60%)
TRUE	126 (63%)	65 (47%)	30 (42%)	58 (54%)	34 (40%)
s_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-77-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-77-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 4

chrom <- 4
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-78-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-78-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-78-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-78-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-78-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-78-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_switches(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
b_l_s
FALSE	161 (80%)	77 (56%)	39 (54%)	76 (71%)	55 (65%)
TRUE	40 (20%)	60 (44%)	33 (46%)	31 (29%)	30 (35%)
e_l_b
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
e_l_s
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	44 (22%)	62 (45%)	34 (47%)	32 (30%)	35 (41%)
TRUE	157 (78%)	75 (55%)	38 (53%)	75 (70%)	50 (59%)
s_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
1 n (%)

table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
b_l_s
FALSE	137 (68%)	62 (45%)	23 (32%)	67 (63%)	39 (46%)
TRUE	64 (32%)	75 (55%)	49 (68%)	40 (37%)	46 (54%)
e_l_b
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
e_l_s
FALSE	201 (100%)	136 (99%)	72 (100%)	107 (100%)	85 (100%)
TRUE	0 (0%)	1 (0.7%)	0 (0%)	0 (0%)	0 (0%)
s_l_b
FALSE	68 (34%)	77 (56%)	53 (74%)	43 (40%)	48 (56%)
TRUE	133 (66%)	60 (44%)	19 (26%)	64 (60%)	37 (44%)
s_l_e
FALSE	0 (0%)	1 (0.7%)	0 (0%)	0 (0%)	0 (0%)
TRUE	201 (100%)	136 (99%)	72 (100%)	107 (100%)	85 (100%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-78-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-78-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 5

chrom <- 5
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-79-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-79-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-79-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-79-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-79-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-79-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_switches(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
b_l_s
FALSE	152 (76%)	77 (56%)	36 (50%)	67 (63%)	47 (55%)
TRUE	49 (24%)	60 (44%)	36 (50%)	40 (37%)	38 (45%)
e_l_b
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
e_l_s
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	56 (28%)	64 (47%)	36 (50%)	42 (39%)	39 (46%)
TRUE	145 (72%)	73 (53%)	36 (50%)	65 (61%)	46 (54%)
s_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
1 n (%)

table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
b_l_s
FALSE	143 (71%)	59 (43%)	29 (40%)	68 (64%)	48 (56%)
TRUE	58 (29%)	78 (57%)	43 (60%)	39 (36%)	37 (44%)
e_l_b
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
e_l_s
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	62 (31%)	80 (58%)	45 (63%)	43 (40%)	40 (47%)
TRUE	139 (69%)	57 (42%)	27 (38%)	64 (60%)	45 (53%)
s_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-79-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-79-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 6

chrom <- 6
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-80-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-80-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-80-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-80-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-80-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-80-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_switches(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
b_l_s
FALSE	144 (72%)	84 (61%)	34 (47%)	68 (64%)	45 (53%)
TRUE	57 (28%)	53 (39%)	38 (53%)	39 (36%)	40 (47%)
e_l_b
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
e_l_s
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	62 (31%)	55 (40%)	38 (53%)	44 (41%)	41 (48%)
TRUE	139 (69%)	82 (60%)	34 (47%)	63 (59%)	44 (52%)
s_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
1 n (%)

table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	0 (0%)	2 (1.5%)	0 (0%)	0 (0%)	0 (0%)
TRUE	201 (100%)	135 (99%)	72 (100%)	107 (100%)	85 (100%)
b_l_s
FALSE	132 (66%)	69 (50%)	30 (42%)	72 (67%)	42 (49%)
TRUE	69 (34%)	68 (50%)	42 (58%)	35 (33%)	43 (51%)
e_l_b
FALSE	201 (100%)	135 (99%)	72 (100%)	107 (100%)	85 (100%)
TRUE	0 (0%)	2 (1.5%)	0 (0%)	0 (0%)	0 (0%)
e_l_s
FALSE	201 (100%)	137 (100%)	72 (100%)	106 (99%)	85 (100%)
TRUE	0 (0%)	0 (0%)	0 (0%)	1 (0.9%)	0 (0%)
s_l_b
FALSE	74 (37%)	69 (50%)	43 (60%)	37 (35%)	45 (53%)
TRUE	127 (63%)	68 (50%)	29 (40%)	70 (65%)	40 (47%)
s_l_e
FALSE	0 (0%)	0 (0%)	0 (0%)	1 (0.9%)	0 (0%)
TRUE	201 (100%)	137 (100%)	72 (100%)	106 (99%)	85 (100%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-80-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-80-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 7

chrom <- 7
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-81-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-81-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-81-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-81-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-81-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-81-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_switches(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	0 (0%)	0 (0%)	0 (0%)	0 (0%)	1 (1.2%)
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	84 (99%)
b_l_s
FALSE	172 (86%)	74 (54%)	31 (43%)	79 (74%)	47 (55%)
TRUE	29 (14%)	63 (46%)	41 (57%)	28 (26%)	38 (45%)
e_l_b
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	84 (99%)
TRUE	0 (0%)	0 (0%)	0 (0%)	0 (0%)	1 (1.2%)
e_l_s
FALSE	201 (100%)	136 (99%)	72 (100%)	107 (100%)	84 (99%)
TRUE	0 (0%)	1 (0.7%)	0 (0%)	0 (0%)	1 (1.2%)
s_l_b
FALSE	29 (14%)	63 (46%)	42 (58%)	36 (34%)	39 (46%)
TRUE	172 (86%)	74 (54%)	30 (42%)	71 (66%)	46 (54%)
s_l_e
FALSE	0 (0%)	1 (0.7%)	0 (0%)	0 (0%)	1 (1.2%)
TRUE	201 (100%)	136 (99%)	72 (100%)	107 (100%)	84 (99%)
1 n (%)

table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	1 (0.5%)	0 (0%)	0 (0%)	1 (0.9%)	1 (1.2%)
TRUE	200 (100%)	137 (100%)	72 (100%)	106 (99%)	84 (99%)
b_l_s
FALSE	149 (74%)	76 (55%)	34 (47%)	73 (68%)	46 (54%)
TRUE	52 (26%)	61 (45%)	38 (53%)	34 (32%)	39 (46%)
e_l_b
FALSE	200 (100%)	137 (100%)	72 (100%)	107 (100%)	84 (99%)
TRUE	1 (0.5%)	0 (0%)	0 (0%)	0 (0%)	1 (1.2%)
e_l_s
FALSE	201 (100%)	135 (99%)	72 (100%)	107 (100%)	84 (99%)
TRUE	0 (0%)	2 (1.5%)	0 (0%)	0 (0%)	1 (1.2%)
s_l_b
FALSE	58 (29%)	62 (45%)	39 (54%)	37 (35%)	40 (47%)
TRUE	143 (71%)	75 (55%)	33 (46%)	70 (65%)	45 (53%)
s_l_e
FALSE	0 (0%)	2 (1.5%)	0 (0%)	0 (0%)	1 (1.2%)
TRUE	201 (100%)	135 (99%)	72 (100%)	107 (100%)	84 (99%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-81-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-81-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 8

chrom <- 8
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-82-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-82-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-82-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-82-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-82-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-82-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_switches(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
b_l_s
FALSE	175 (87%)	105 (77%)	63 (88%)	90 (84%)	63 (74%)
TRUE	26 (13%)	32 (23%)	9 (13%)	17 (16%)	22 (26%)
e_l_b
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
e_l_s
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	31 (15%)	35 (26%)	10 (14%)	23 (21%)	25 (29%)
TRUE	170 (85%)	102 (74%)	62 (86%)	84 (79%)	60 (71%)
s_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
1 n (%)

table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	2 (1.0%)	1 (0.7%)	0 (0%)	1 (0.9%)	0 (0%)
TRUE	199 (99%)	136 (99%)	72 (100%)	106 (99%)	85 (100%)
b_l_s
FALSE	131 (65%)	53 (39%)	29 (40%)	59 (55%)	46 (54%)
TRUE	70 (35%)	84 (61%)	43 (60%)	48 (45%)	39 (46%)
e_l_b
FALSE	199 (99%)	136 (99%)	72 (100%)	107 (100%)	85 (100%)
TRUE	2 (1.0%)	1 (0.7%)	0 (0%)	0 (0%)	0 (0%)
e_l_s
FALSE	199 (99%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
TRUE	2 (1.0%)	0 (0%)	0 (0%)	0 (0%)	0 (0%)
s_l_b
FALSE	76 (38%)	87 (64%)	45 (63%)	50 (47%)	43 (51%)
TRUE	125 (62%)	50 (36%)	27 (38%)	57 (53%)	42 (49%)
s_l_e
FALSE	2 (1.0%)	0 (0%)	0 (0%)	0 (0%)	0 (0%)
TRUE	199 (99%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-82-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-82-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 9

chrom <- 9
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-83-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-83-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-83-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-83-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-83-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-83-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_switches(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	0 (0%)	3 (2.2%)	0 (0%)	2 (1.9%)	1 (1.2%)
TRUE	201 (100%)	134 (98%)	72 (100%)	105 (98%)	84 (99%)
b_l_s
FALSE	165 (82%)	92 (67%)	42 (58%)	79 (74%)	58 (68%)
TRUE	36 (18%)	45 (33%)	30 (42%)	28 (26%)	27 (32%)
e_l_b
FALSE	201 (100%)	135 (99%)	72 (100%)	105 (98%)	84 (99%)
TRUE	0 (0%)	2 (1.5%)	0 (0%)	2 (1.9%)	1 (1.2%)
e_l_s
FALSE	199 (99%)	136 (99%)	72 (100%)	107 (100%)	84 (99%)
TRUE	2 (1.0%)	1 (0.7%)	0 (0%)	0 (0%)	1 (1.2%)
s_l_b
FALSE	38 (19%)	45 (33%)	31 (43%)	31 (29%)	32 (38%)
TRUE	163 (81%)	92 (67%)	41 (57%)	76 (71%)	53 (62%)
s_l_e
FALSE	2 (1.0%)	1 (0.7%)	0 (0%)	0 (0%)	1 (1.2%)
TRUE	199 (99%)	136 (99%)	72 (100%)	107 (100%)	84 (99%)
1 n (%)

table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	2 (1.0%)	0 (0%)	0 (0%)	4 (3.7%)	2 (2.4%)
TRUE	199 (99%)	137 (100%)	72 (100%)	103 (96%)	83 (98%)
b_l_s
FALSE	151 (75%)	72 (53%)	39 (54%)	73 (68%)	50 (59%)
TRUE	50 (25%)	65 (47%)	33 (46%)	34 (32%)	35 (41%)
e_l_b
FALSE	200 (100%)	137 (100%)	72 (100%)	104 (97%)	84 (99%)
TRUE	1 (0.5%)	0 (0%)	0 (0%)	3 (2.8%)	1 (1.2%)
e_l_s
FALSE	200 (100%)	135 (99%)	72 (100%)	106 (99%)	83 (98%)
TRUE	1 (0.5%)	2 (1.5%)	0 (0%)	1 (0.9%)	2 (2.4%)
s_l_b
FALSE	56 (28%)	68 (50%)	36 (50%)	39 (36%)	36 (42%)
TRUE	145 (72%)	69 (50%)	36 (50%)	68 (64%)	49 (58%)
s_l_e
FALSE	1 (0.5%)	2 (1.5%)	0 (0%)	1 (0.9%)	2 (2.4%)
TRUE	200 (100%)	135 (99%)	72 (100%)	106 (99%)	83 (98%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-83-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-83-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 10

chrom <- 10
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-84-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-84-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-84-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-84-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-84-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-84-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_switches(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
b_l_s
FALSE	152 (76%)	79 (58%)	37 (51%)	79 (74%)	51 (60%)
TRUE	49 (24%)	58 (42%)	35 (49%)	28 (26%)	34 (40%)
e_l_b
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
e_l_s
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	53 (26%)	59 (43%)	35 (49%)	30 (28%)	37 (44%)
TRUE	148 (74%)	78 (57%)	37 (51%)	77 (72%)	48 (56%)
s_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
1 n (%)

table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
b_l_s
FALSE	153 (76%)	84 (61%)	33 (46%)	78 (73%)	47 (55%)
TRUE	48 (24%)	53 (39%)	39 (54%)	29 (27%)	38 (45%)
e_l_b
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
e_l_s
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	53 (26%)	58 (42%)	40 (56%)	32 (30%)	40 (47%)
TRUE	148 (74%)	79 (58%)	32 (44%)	75 (70%)	45 (53%)
s_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-84-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-84-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 11

chrom <- 11
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-85-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-85-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-85-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-85-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-85-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-85-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_switches(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	0 (0%)	1 (0.7%)	0 (0%)	0 (0%)	0 (0%)
TRUE	201 (100%)	136 (99%)	72 (100%)	107 (100%)	85 (100%)
b_l_s
FALSE	144 (72%)	78 (57%)	39 (54%)	68 (64%)	50 (59%)
TRUE	57 (28%)	59 (43%)	33 (46%)	39 (36%)	35 (41%)
e_l_b
FALSE	201 (100%)	136 (99%)	72 (100%)	107 (100%)	85 (100%)
TRUE	0 (0%)	1 (0.7%)	0 (0%)	0 (0%)	0 (0%)
e_l_s
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	62 (31%)	61 (45%)	35 (49%)	44 (41%)	36 (42%)
TRUE	139 (69%)	76 (55%)	37 (51%)	63 (59%)	49 (58%)
s_l_e
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
1 n (%)

table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	3 (1.5%)	1 (0.7%)	0 (0%)	0 (0%)	0 (0%)
TRUE	198 (99%)	136 (99%)	72 (100%)	107 (100%)	85 (100%)
b_l_s
FALSE	131 (65%)	68 (50%)	37 (51%)	69 (64%)	52 (61%)
TRUE	70 (35%)	69 (50%)	35 (49%)	38 (36%)	33 (39%)
e_l_b
FALSE	198 (99%)	136 (99%)	72 (100%)	107 (100%)	85 (100%)
TRUE	3 (1.5%)	1 (0.7%)	0 (0%)	0 (0%)	0 (0%)
e_l_s
FALSE	200 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
TRUE	1 (0.5%)	0 (0%)	0 (0%)	0 (0%)	0 (0%)
s_l_b
FALSE	75 (37%)	74 (54%)	37 (51%)	39 (36%)	37 (44%)
TRUE	126 (63%)	63 (46%)	35 (49%)	68 (64%)	48 (56%)
s_l_e
FALSE	1 (0.5%)	0 (0%)	0 (0%)	0 (0%)	0 (0%)
TRUE	200 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-85-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-85-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 12

chrom <- 12
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-86-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-86-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-86-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-86-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-86-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-86-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_switches(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	1 (0.5%)	0 (0%)	0 (0%)	0 (0%)	1 (1.2%)
TRUE	200 (100%)	137 (100%)	72 (100%)	107 (100%)	84 (99%)
b_l_s
FALSE	147 (73%)	79 (58%)	35 (49%)	71 (66%)	44 (52%)
TRUE	54 (27%)	58 (42%)	37 (51%)	36 (34%)	41 (48%)
e_l_b
FALSE	200 (100%)	137 (100%)	72 (100%)	107 (100%)	84 (99%)
TRUE	1 (0.5%)	0 (0%)	0 (0%)	0 (0%)	1 (1.2%)
e_l_s
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	84 (99%)
TRUE	0 (0%)	0 (0%)	0 (0%)	0 (0%)	1 (1.2%)
s_l_b
FALSE	58 (29%)	61 (45%)	39 (54%)	40 (37%)	43 (51%)
TRUE	143 (71%)	76 (55%)	33 (46%)	67 (63%)	42 (49%)
s_l_e
FALSE	0 (0%)	1 (0.7%)	0 (0%)	0 (0%)	1 (1.2%)
TRUE	201 (100%)	136 (99%)	72 (100%)	107 (100%)	84 (99%)
1 n (%)

table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	0 (0%)	0 (0%)	0 (0%)	0 (0%)	1 (1.2%)
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	84 (99%)
b_l_s
FALSE	143 (71%)	69 (50%)	33 (46%)	65 (61%)	45 (53%)
TRUE	58 (29%)	68 (50%)	39 (54%)	42 (39%)	40 (47%)
e_l_b
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	84 (99%)
TRUE	0 (0%)	0 (0%)	0 (0%)	0 (0%)	1 (1.2%)
e_l_s
FALSE	200 (100%)	137 (100%)	72 (100%)	106 (99%)	84 (99%)
TRUE	1 (0.5%)	0 (0%)	0 (0%)	1 (0.9%)	1 (1.2%)
s_l_b
FALSE	61 (30%)	72 (53%)	42 (58%)	45 (42%)	42 (49%)
TRUE	140 (70%)	65 (47%)	30 (42%)	62 (58%)	43 (51%)
s_l_e
FALSE	1 (0.5%)	2 (1.5%)	0 (0%)	1 (0.9%)	1 (1.2%)
TRUE	200 (100%)	135 (99%)	72 (100%)	106 (99%)	84 (99%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-86-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-86-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 13

chrom <- 13
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-87-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-87-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-87-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-87-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-87-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-87-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_switches(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	1 (0.5%)	1 (0.7%)	1 (1.4%)	2 (1.9%)	1 (1.2%)
TRUE	200 (100%)	136 (99%)	71 (99%)	105 (98%)	84 (99%)
b_l_s
FALSE	148 (74%)	80 (58%)	41 (57%)	68 (64%)	50 (59%)
TRUE	53 (26%)	57 (42%)	31 (43%)	39 (36%)	35 (41%)
e_l_b
FALSE	201 (100%)	136 (99%)	71 (99%)	105 (98%)	84 (99%)
TRUE	0 (0%)	1 (0.7%)	1 (1.4%)	2 (1.9%)	1 (1.2%)
e_l_s
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	84 (99%)
TRUE	0 (0%)	0 (0%)	0 (0%)	0 (0%)	1 (1.2%)
s_l_b
FALSE	62 (31%)	63 (46%)	31 (43%)	40 (37%)	39 (46%)
TRUE	139 (69%)	74 (54%)	41 (57%)	67 (63%)	46 (54%)
s_l_e
FALSE	0 (0%)	0 (0%)	0 (0%)	0 (0%)	1 (1.2%)
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	84 (99%)
1 n (%)

table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	1 (0.5%)	1 (0.7%)	0 (0%)	2 (1.9%)	1 (1.2%)
TRUE	200 (100%)	136 (99%)	72 (100%)	105 (98%)	84 (99%)
b_l_s
FALSE	128 (64%)	61 (45%)	35 (49%)	65 (61%)	42 (49%)
TRUE	73 (36%)	76 (55%)	37 (51%)	42 (39%)	43 (51%)
e_l_b
FALSE	200 (100%)	136 (99%)	72 (100%)	105 (98%)	84 (99%)
TRUE	1 (0.5%)	1 (0.7%)	0 (0%)	2 (1.9%)	1 (1.2%)
e_l_s
FALSE	200 (100%)	135 (99%)	72 (100%)	105 (98%)	85 (100%)
TRUE	1 (0.5%)	2 (1.5%)	0 (0%)	2 (1.9%)	0 (0%)
s_l_b
FALSE	81 (40%)	82 (60%)	39 (54%)	45 (42%)	48 (56%)
TRUE	120 (60%)	55 (40%)	33 (46%)	62 (58%)	37 (44%)
s_l_e
FALSE	1 (0.5%)	2 (1.5%)	0 (0%)	2 (1.9%)	0 (0%)
TRUE	200 (100%)	135 (99%)	72 (100%)	105 (98%)	85 (100%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-87-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-87-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 14

chrom <- 14
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-88-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-88-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-88-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-88-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-88-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-88-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_switches(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	1 (0.5%)	1 (0.7%)	0 (0%)	0 (0%)	0 (0%)
TRUE	200 (100%)	136 (99%)	72 (100%)	107 (100%)	85 (100%)
b_l_s
FALSE	146 (73%)	67 (49%)	38 (53%)	65 (61%)	45 (53%)
TRUE	55 (27%)	70 (51%)	34 (47%)	42 (39%)	40 (47%)
e_l_b
FALSE	200 (100%)	136 (99%)	72 (100%)	107 (100%)	85 (100%)
TRUE	1 (0.5%)	1 (0.7%)	0 (0%)	0 (0%)	0 (0%)
e_l_s
FALSE	200 (100%)	135 (99%)	72 (100%)	106 (99%)	85 (100%)
TRUE	1 (0.5%)	2 (1.5%)	0 (0%)	1 (0.9%)	0 (0%)
s_l_b
FALSE	61 (30%)	75 (55%)	37 (51%)	46 (43%)	41 (48%)
TRUE	140 (70%)	62 (45%)	35 (49%)	61 (57%)	44 (52%)
s_l_e
FALSE	1 (0.5%)	2 (1.5%)	0 (0%)	1 (0.9%)	0 (0%)
TRUE	200 (100%)	135 (99%)	72 (100%)	106 (99%)	85 (100%)
1 n (%)

table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	2 (1.0%)	1 (0.7%)	0 (0%)	1 (0.9%)	0 (0%)
TRUE	199 (99%)	136 (99%)	72 (100%)	106 (99%)	85 (100%)
b_l_s
FALSE	127 (63%)	68 (50%)	37 (51%)	64 (60%)	41 (48%)
TRUE	74 (37%)	69 (50%)	35 (49%)	43 (40%)	44 (52%)
e_l_b
FALSE	199 (99%)	137 (100%)	72 (100%)	106 (99%)	85 (100%)
TRUE	2 (1.0%)	0 (0%)	0 (0%)	1 (0.9%)	0 (0%)
e_l_s
FALSE	200 (100%)	137 (100%)	71 (99%)	106 (99%)	84 (99%)
TRUE	1 (0.5%)	0 (0%)	1 (1.4%)	1 (0.9%)	1 (1.2%)
s_l_b
FALSE	80 (40%)	74 (54%)	41 (57%)	45 (42%)	46 (54%)
TRUE	121 (60%)	63 (46%)	31 (43%)	62 (58%)	39 (46%)
s_l_e
FALSE	3 (1.5%)	0 (0%)	1 (1.4%)	1 (0.9%)	2 (2.4%)
TRUE	198 (99%)	137 (100%)	71 (99%)	106 (99%)	83 (98%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-88-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-88-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 15

chrom <- 15
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-89-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-89-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-89-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-89-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-89-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-89-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_switches(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	6 (3.0%)	2 (1.5%)	0 (0%)	2 (1.9%)	1 (1.2%)
TRUE	195 (97%)	135 (99%)	72 (100%)	105 (98%)	84 (99%)
b_l_s
FALSE	138 (69%)	77 (56%)	41 (57%)	74 (69%)	53 (62%)
TRUE	63 (31%)	60 (44%)	31 (43%)	33 (31%)	32 (38%)
e_l_b
FALSE	196 (98%)	136 (99%)	72 (100%)	105 (98%)	84 (99%)
TRUE	5 (2.5%)	1 (0.7%)	0 (0%)	2 (1.9%)	1 (1.2%)
e_l_s
FALSE	199 (99%)	133 (97%)	72 (100%)	107 (100%)	85 (100%)
TRUE	2 (1.0%)	4 (2.9%)	0 (0%)	0 (0%)	0 (0%)
s_l_b
FALSE	64 (32%)	64 (47%)	31 (43%)	39 (36%)	36 (42%)
TRUE	137 (68%)	73 (53%)	41 (57%)	68 (64%)	49 (58%)
s_l_e
FALSE	2 (1.0%)	4 (2.9%)	0 (0%)	0 (0%)	0 (0%)
TRUE	199 (99%)	133 (97%)	72 (100%)	107 (100%)	85 (100%)
1 n (%)

table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	4 (2.0%)	2 (1.5%)	1 (1.4%)	2 (1.9%)	0 (0%)
TRUE	197 (98%)	135 (99%)	71 (99%)	105 (98%)	85 (100%)
b_l_s
FALSE	138 (69%)	69 (50%)	34 (47%)	70 (65%)	37 (44%)
TRUE	63 (31%)	68 (50%)	38 (53%)	37 (35%)	48 (56%)
e_l_b
FALSE	197 (98%)	135 (99%)	71 (99%)	106 (99%)	85 (100%)
TRUE	4 (2.0%)	2 (1.5%)	1 (1.4%)	1 (0.9%)	0 (0%)
e_l_s
FALSE	200 (100%)	136 (99%)	72 (100%)	106 (99%)	83 (98%)
TRUE	1 (0.5%)	1 (0.7%)	0 (0%)	1 (0.9%)	2 (2.4%)
s_l_b
FALSE	68 (34%)	73 (53%)	38 (53%)	42 (39%)	51 (60%)
TRUE	133 (66%)	64 (47%)	34 (47%)	65 (61%)	34 (40%)
s_l_e
FALSE	1 (0.5%)	1 (0.7%)	1 (1.4%)	1 (0.9%)	2 (2.4%)
TRUE	200 (100%)	136 (99%)	71 (99%)	106 (99%)	83 (98%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-89-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-89-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 16

chrom <- 16
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-90-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-90-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-90-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-90-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-90-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-90-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_switches(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	1 (0.5%)	1 (0.7%)	0 (0%)	1 (0.9%)	0 (0%)
TRUE	200 (100%)	136 (99%)	72 (100%)	106 (99%)	85 (100%)
b_l_s
FALSE	150 (75%)	76 (55%)	47 (65%)	70 (65%)	51 (60%)
TRUE	51 (25%)	61 (45%)	25 (35%)	37 (35%)	34 (40%)
e_l_b
FALSE	200 (100%)	137 (100%)	72 (100%)	106 (99%)	85 (100%)
TRUE	1 (0.5%)	0 (0%)	0 (0%)	1 (0.9%)	0 (0%)
e_l_s
FALSE	201 (100%)	137 (100%)	72 (100%)	106 (99%)	85 (100%)
TRUE	0 (0%)	0 (0%)	0 (0%)	1 (0.9%)	0 (0%)
s_l_b
FALSE	55 (27%)	62 (45%)	27 (38%)	41 (38%)	39 (46%)
TRUE	146 (73%)	75 (55%)	45 (63%)	66 (62%)	46 (54%)
s_l_e
FALSE	0 (0%)	0 (0%)	0 (0%)	2 (1.9%)	0 (0%)
TRUE	201 (100%)	137 (100%)	72 (100%)	105 (98%)	85 (100%)
1 n (%)

table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	1 (0.5%)	0 (0%)	1 (1.4%)	0 (0%)	3 (3.5%)
TRUE	200 (100%)	137 (100%)	71 (99%)	107 (100%)	82 (96%)
b_l_s
FALSE	146 (73%)	67 (49%)	27 (38%)	51 (48%)	39 (46%)
TRUE	55 (27%)	70 (51%)	45 (63%)	56 (52%)	46 (54%)
e_l_b
FALSE	200 (100%)	137 (100%)	71 (99%)	107 (100%)	82 (96%)
TRUE	1 (0.5%)	0 (0%)	1 (1.4%)	0 (0%)	3 (3.5%)
e_l_s
FALSE	200 (100%)	135 (99%)	72 (100%)	107 (100%)	80 (94%)
TRUE	1 (0.5%)	2 (1.5%)	0 (0%)	0 (0%)	5 (5.9%)
s_l_b
FALSE	59 (29%)	74 (54%)	46 (64%)	57 (53%)	47 (55%)
TRUE	142 (71%)	63 (46%)	26 (36%)	50 (47%)	38 (45%)
s_l_e
FALSE	1 (0.5%)	3 (2.2%)	0 (0%)	0 (0%)	6 (7.1%)
TRUE	200 (100%)	134 (98%)	72 (100%)	107 (100%)	79 (93%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-90-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-90-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 17

chrom <- 17
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-91-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-91-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-91-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-91-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-91-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-91-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_switches(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	0 (0%)	4 (2.9%)	0 (0%)	1 (0.9%)	0 (0%)
TRUE	201 (100%)	133 (97%)	72 (100%)	106 (99%)	85 (100%)
b_l_s
FALSE	156 (78%)	99 (72%)	41 (57%)	77 (72%)	52 (61%)
TRUE	45 (22%)	38 (28%)	31 (43%)	30 (28%)	33 (39%)
e_l_b
FALSE	201 (100%)	134 (98%)	72 (100%)	106 (99%)	85 (100%)
TRUE	0 (0%)	3 (2.2%)	0 (0%)	1 (0.9%)	0 (0%)
e_l_s
FALSE	200 (100%)	136 (99%)	71 (99%)	107 (100%)	85 (100%)
TRUE	1 (0.5%)	1 (0.7%)	1 (1.4%)	0 (0%)	0 (0%)
s_l_b
FALSE	48 (24%)	44 (32%)	34 (47%)	36 (34%)	35 (41%)
TRUE	153 (76%)	93 (68%)	38 (53%)	71 (66%)	50 (59%)
s_l_e
FALSE	1 (0.5%)	1 (0.7%)	1 (1.4%)	0 (0%)	0 (0%)
TRUE	200 (100%)	136 (99%)	71 (99%)	107 (100%)	85 (100%)
1 n (%)

table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	1 (0.5%)	1 (0.7%)	0 (0%)	1 (0.9%)	0 (0%)
TRUE	200 (100%)	136 (99%)	72 (100%)	106 (99%)	85 (100%)
b_l_s
FALSE	133 (66%)	85 (62%)	32 (44%)	67 (63%)	56 (66%)
TRUE	68 (34%)	52 (38%)	40 (56%)	40 (37%)	29 (34%)
e_l_b
FALSE	201 (100%)	136 (99%)	72 (100%)	106 (99%)	85 (100%)
TRUE	0 (0%)	1 (0.7%)	0 (0%)	1 (0.9%)	0 (0%)
e_l_s
FALSE	199 (99%)	136 (99%)	72 (100%)	106 (99%)	85 (100%)
TRUE	2 (1.0%)	1 (0.7%)	0 (0%)	1 (0.9%)	0 (0%)
s_l_b
FALSE	71 (35%)	61 (45%)	43 (60%)	43 (40%)	31 (36%)
TRUE	130 (65%)	76 (55%)	29 (40%)	64 (60%)	54 (64%)
s_l_e
FALSE	2 (1.0%)	1 (0.7%)	0 (0%)	1 (0.9%)	1 (1.2%)
TRUE	199 (99%)	136 (99%)	72 (100%)	106 (99%)	84 (99%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-91-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-91-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 18

chrom <- 18
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-92-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-92-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-92-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-92-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-92-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-92-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_switches(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	2 (1.0%)	1 (0.7%)	0 (0%)	0 (0%)	0 (0%)
TRUE	199 (99%)	136 (99%)	72 (100%)	107 (100%)	85 (100%)
b_l_s
FALSE	139 (69%)	74 (54%)	37 (51%)	60 (56%)	50 (59%)
TRUE	62 (31%)	63 (46%)	35 (49%)	47 (44%)	35 (41%)
e_l_b
FALSE	201 (100%)	136 (99%)	72 (100%)	107 (100%)	85 (100%)
TRUE	0 (0%)	1 (0.7%)	0 (0%)	0 (0%)	0 (0%)
e_l_s
FALSE	200 (100%)	136 (99%)	72 (100%)	106 (99%)	85 (100%)
TRUE	1 (0.5%)	1 (0.7%)	0 (0%)	1 (0.9%)	0 (0%)
s_l_b
FALSE	65 (32%)	66 (48%)	40 (56%)	53 (50%)	38 (45%)
TRUE	136 (68%)	71 (52%)	32 (44%)	54 (50%)	47 (55%)
s_l_e
FALSE	1 (0.5%)	2 (1.5%)	0 (0%)	1 (0.9%)	0 (0%)
TRUE	200 (100%)	135 (99%)	72 (100%)	106 (99%)	85 (100%)
1 n (%)

table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	4 (2.0%)	5 (3.6%)	0 (0%)	3 (2.8%)	1 (1.2%)
TRUE	197 (98%)	132 (96%)	72 (100%)	104 (97%)	84 (99%)
b_l_s
FALSE	130 (65%)	72 (53%)	36 (50%)	56 (52%)	50 (59%)
TRUE	71 (35%)	65 (47%)	36 (50%)	51 (48%)	35 (41%)
e_l_b
FALSE	197 (98%)	134 (98%)	72 (100%)	104 (97%)	84 (99%)
TRUE	4 (2.0%)	3 (2.2%)	0 (0%)	3 (2.8%)	1 (1.2%)
e_l_s
FALSE	200 (100%)	130 (95%)	70 (97%)	106 (99%)	85 (100%)
TRUE	1 (0.5%)	7 (5.1%)	2 (2.8%)	1 (0.9%)	0 (0%)
s_l_b
FALSE	79 (39%)	70 (51%)	37 (51%)	57 (53%)	38 (45%)
TRUE	122 (61%)	67 (49%)	35 (49%)	50 (47%)	47 (55%)
s_l_e
FALSE	1 (0.5%)	7 (5.1%)	2 (2.8%)	2 (1.9%)	0 (0%)
TRUE	200 (100%)	130 (95%)	70 (97%)	105 (98%)	85 (100%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-92-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-92-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 19

chrom <- 19
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-93-1.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-93-2.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-93-3.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-93-4.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-93-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-93-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_switches(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	2 (1.0%)	1 (0.7%)	1 (1.4%)	0 (0%)	4 (4.7%)
TRUE	199 (99%)	136 (99%)	71 (99%)	107 (100%)	81 (95%)
b_l_s
FALSE	153 (76%)	89 (65%)	40 (56%)	60 (56%)	60 (71%)
TRUE	48 (24%)	48 (35%)	32 (44%)	47 (44%)	25 (29%)
e_l_b
FALSE	199 (99%)	136 (99%)	72 (100%)	107 (100%)	82 (96%)
TRUE	2 (1.0%)	1 (0.7%)	0 (0%)	0 (0%)	3 (3.5%)
e_l_s
FALSE	201 (100%)	136 (99%)	72 (100%)	107 (100%)	82 (96%)
TRUE	0 (0%)	1 (0.7%)	0 (0%)	0 (0%)	3 (3.5%)
s_l_b
FALSE	55 (27%)	51 (37%)	32 (44%)	50 (47%)	28 (33%)
TRUE	146 (73%)	86 (63%)	40 (56%)	57 (53%)	57 (67%)
s_l_e
FALSE	0 (0%)	2 (1.5%)	0 (0%)	0 (0%)	3 (3.5%)
TRUE	201 (100%)	135 (99%)	72 (100%)	107 (100%)	82 (96%)
1 n (%)

table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	4 (2.0%)	8 (5.8%)	1 (1.4%)	3 (2.8%)	0 (0%)
TRUE	197 (98%)	129 (94%)	71 (99%)	104 (97%)	85 (100%)
b_l_s
FALSE	139 (69%)	83 (61%)	37 (51%)	67 (63%)	47 (55%)
TRUE	62 (31%)	54 (39%)	35 (49%)	40 (37%)	38 (45%)
e_l_b
FALSE	197 (98%)	130 (95%)	72 (100%)	104 (97%)	85 (100%)
TRUE	4 (2.0%)	7 (5.1%)	0 (0%)	3 (2.8%)	0 (0%)
e_l_s
FALSE	201 (100%)	132 (96%)	70 (97%)	107 (100%)	80 (94%)
TRUE	0 (0%)	5 (3.6%)	2 (2.8%)	0 (0%)	5 (5.9%)
s_l_b
FALSE	70 (35%)	57 (42%)	37 (51%)	46 (43%)	38 (45%)
TRUE	131 (65%)	80 (58%)	35 (49%)	61 (57%)	47 (55%)
s_l_e
FALSE	0 (0%)	5 (3.6%)	2 (2.8%)	1 (0.9%)	6 (7.1%)
TRUE	201 (100%)	132 (96%)	70 (97%)	106 (99%)	79 (93%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-93-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-93-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 20

chrom <- 20
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-94-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-94-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-94-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-94-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-94-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-94-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_switches(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	3 (1.5%)	2 (1.5%)	2 (2.8%)	3 (2.8%)	0 (0%)
TRUE	198 (99%)	135 (99%)	70 (97%)	104 (97%)	85 (100%)
b_l_s
FALSE	164 (82%)	78 (57%)	44 (61%)	76 (71%)	54 (64%)
TRUE	37 (18%)	59 (43%)	28 (39%)	31 (29%)	31 (36%)
e_l_b
FALSE	199 (99%)	137 (100%)	70 (97%)	104 (97%)	85 (100%)
TRUE	2 (1.0%)	0 (0%)	2 (2.8%)	3 (2.8%)	0 (0%)
e_l_s
FALSE	201 (100%)	134 (98%)	72 (100%)	106 (99%)	85 (100%)
TRUE	0 (0%)	3 (2.2%)	0 (0%)	1 (0.9%)	0 (0%)
s_l_b
FALSE	40 (20%)	63 (46%)	31 (43%)	35 (33%)	34 (40%)
TRUE	161 (80%)	74 (54%)	41 (57%)	72 (67%)	51 (60%)
s_l_e
FALSE	0 (0%)	3 (2.2%)	0 (0%)	1 (0.9%)	0 (0%)
TRUE	201 (100%)	134 (98%)	72 (100%)	106 (99%)	85 (100%)
1 n (%)

table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	4 (2.0%)	5 (3.6%)	2 (2.8%)	4 (3.7%)	0 (0%)
TRUE	197 (98%)	132 (96%)	70 (97%)	103 (96%)	85 (100%)
b_l_s
FALSE	145 (72%)	77 (56%)	40 (56%)	67 (63%)	52 (61%)
TRUE	56 (28%)	60 (44%)	32 (44%)	40 (37%)	33 (39%)
e_l_b
FALSE	199 (99%)	134 (98%)	70 (97%)	103 (96%)	85 (100%)
TRUE	2 (1.0%)	3 (2.2%)	2 (2.8%)	4 (3.7%)	0 (0%)
e_l_s
FALSE	200 (100%)	135 (99%)	71 (99%)	107 (100%)	84 (99%)
TRUE	1 (0.5%)	2 (1.5%)	1 (1.4%)	0 (0%)	1 (1.2%)
s_l_b
FALSE	59 (29%)	63 (46%)	32 (44%)	42 (39%)	34 (40%)
TRUE	142 (71%)	74 (54%)	40 (56%)	65 (61%)	51 (60%)
s_l_e
FALSE	1 (0.5%)	2 (1.5%)	1 (1.4%)	0 (0%)	1 (1.2%)
TRUE	200 (100%)	135 (99%)	71 (99%)	107 (100%)	84 (99%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-94-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-94-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 21

chrom <- 21
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-95-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-95-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-95-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-95-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

table_switches(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	7 (3.5%)	12 (8.8%)	6 (8.3%)	14 (13%)	6 (7.1%)
TRUE	194 (97%)	125 (91%)	66 (92%)	93 (87%)	79 (93%)
b_l_s
FALSE	125 (62%)	69 (50%)	39 (54%)	67 (63%)	48 (56%)
TRUE	76 (38%)	68 (50%)	33 (46%)	40 (37%)	37 (44%)
e_l_b
FALSE	196 (98%)	127 (93%)	67 (93%)	98 (92%)	81 (95%)
TRUE	5 (2.5%)	10 (7.3%)	5 (6.9%)	9 (8.4%)	4 (4.7%)
e_l_s
FALSE	197 (98%)	123 (90%)	69 (96%)	99 (93%)	84 (99%)
TRUE	4 (2.0%)	14 (10%)	3 (4.2%)	8 (7.5%)	1 (1.2%)
s_l_b
FALSE	80 (40%)	73 (53%)	35 (49%)	45 (42%)	37 (44%)
TRUE	121 (60%)	64 (47%)	37 (51%)	62 (58%)	48 (56%)
s_l_e
FALSE	5 (2.5%)	15 (11%)	3 (4.2%)	10 (9.3%)	2 (2.4%)
TRUE	196 (98%)	122 (89%)	69 (96%)	97 (91%)	83 (98%)
1 n (%)

table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	13 (6.5%)	15 (11%)	5 (6.9%)	18 (17%)	5 (5.9%)
TRUE	188 (94%)	122 (89%)	67 (93%)	89 (83%)	80 (94%)
b_l_s
FALSE	122 (61%)	69 (50%)	40 (56%)	56 (52%)	37 (44%)
TRUE	79 (39%)	68 (50%)	32 (44%)	51 (48%)	48 (56%)
e_l_b
FALSE	192 (96%)	125 (91%)	68 (94%)	89 (83%)	80 (94%)
TRUE	9 (4.5%)	12 (8.8%)	4 (5.6%)	18 (17%)	5 (5.9%)
e_l_s
FALSE	191 (95%)	119 (87%)	69 (96%)	101 (94%)	82 (96%)
TRUE	10 (5.0%)	18 (13%)	3 (4.2%)	6 (5.6%)	3 (3.5%)
s_l_b
FALSE	91 (45%)	77 (56%)	36 (50%)	54 (50%)	51 (60%)
TRUE	110 (55%)	60 (44%)	36 (50%)	53 (50%)	34 (40%)
s_l_e
FALSE	14 (7.0%)	20 (15%)	3 (4.2%)	9 (8.4%)	3 (3.5%)
TRUE	187 (93%)	117 (85%)	69 (96%)	98 (92%)	82 (96%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Chromosome 22

chrom <- 22
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-96-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-96-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-96-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-96-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

table_switches(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	9 (4.5%)	5 (3.6%)	3 (4.2%)	6 (5.6%)	4 (4.7%)
TRUE	192 (96%)	132 (96%)	69 (96%)	101 (94%)	81 (95%)
b_l_s
FALSE	153 (76%)	82 (60%)	42 (58%)	73 (68%)	57 (67%)
TRUE	48 (24%)	55 (40%)	30 (42%)	34 (32%)	28 (33%)
e_l_b
FALSE	195 (97%)	132 (96%)	70 (97%)	101 (94%)	81 (95%)
TRUE	6 (3.0%)	5 (3.6%)	2 (2.8%)	6 (5.6%)	4 (4.7%)
e_l_s
FALSE	198 (99%)	133 (97%)	70 (97%)	106 (99%)	83 (98%)
TRUE	3 (1.5%)	4 (2.9%)	2 (2.8%)	1 (0.9%)	2 (2.4%)
s_l_b
FALSE	57 (28%)	59 (43%)	32 (44%)	36 (34%)	30 (35%)
TRUE	144 (72%)	78 (57%)	40 (56%)	71 (66%)	55 (65%)
s_l_e
FALSE	4 (2.0%)	5 (3.6%)	2 (2.8%)	3 (2.8%)	3 (3.5%)
TRUE	197 (98%)	132 (96%)	70 (97%)	104 (97%)	82 (96%)
1 n (%)

table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	10 (5.0%)	13 (9.5%)	4 (5.6%)	16 (15%)	10 (12%)
TRUE	191 (95%)	124 (91%)	68 (94%)	91 (85%)	75 (88%)
b_l_s
FALSE	149 (74%)	79 (58%)	41 (57%)	57 (53%)	53 (62%)
TRUE	52 (26%)	58 (42%)	31 (43%)	50 (47%)	32 (38%)
e_l_b
FALSE	195 (97%)	126 (92%)	68 (94%)	94 (88%)	76 (89%)
TRUE	6 (3.0%)	11 (8.0%)	4 (5.6%)	13 (12%)	9 (11%)
e_l_s
FALSE	198 (99%)	130 (95%)	68 (94%)	94 (88%)	76 (89%)
TRUE	3 (1.5%)	7 (5.1%)	4 (5.6%)	13 (12%)	9 (11%)
s_l_b
FALSE	56 (28%)	65 (47%)	34 (47%)	54 (50%)	33 (39%)
TRUE	145 (72%)	72 (53%)	38 (53%)	53 (50%)	52 (61%)
s_l_e
FALSE	3 (1.5%)	7 (5.1%)	4 (5.6%)	14 (13%)	9 (11%)
TRUE	198 (99%)	130 (95%)	68 (94%)	93 (87%)	76 (89%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

Chromosome X

plot_switches(df_switch_x, "Beagle", "Eagle", "pop", "X")

Past versions of unnamed-chunk-97-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_x, "Beagle", "SHAPEIT", "pop", "X")

Past versions of unnamed-chunk-97-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switches(df_switch_x, "SHAPEIT", "Eagle", "pop", "X")

Past versions of unnamed-chunk-97-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

table_switches(df_switch_x, "pop")

Characteristic	AFR N = 2001	AMR N = 2001	EAS N = 2001	EUR N = 2001	SAS N = 2001
b_l_e
FALSE	0 (0%)	0 (0%)	1 (0.5%)	0 (0%)	0 (0%)
TRUE	200 (100%)	200 (100%)	199 (100%)	200 (100%)	200 (100%)
b_l_s
FALSE	174 (87%)	150 (75%)	163 (82%)	162 (81%)	166 (83%)
TRUE	26 (13%)	50 (25%)	37 (19%)	38 (19%)	34 (17%)
e_l_b
FALSE	200 (100%)	200 (100%)	199 (100%)	200 (100%)	200 (100%)
TRUE	0 (0%)	0 (0%)	1 (0.5%)	0 (0%)	0 (0%)
e_l_s
FALSE	200 (100%)	200 (100%)	200 (100%)	200 (100%)	200 (100%)
s_l_b
FALSE	30 (15%)	58 (29%)	45 (23%)	49 (25%)	39 (20%)
TRUE	170 (85%)	142 (71%)	155 (78%)	151 (76%)	161 (81%)
s_l_e
TRUE	200 (100%)	200 (100%)	200 (100%)	200 (100%)	200 (100%)
1 n (%)

cross_meth_plot(df_switch_x, "Switches", plot_switches, "pop", "X")

Past versions of unnamed-chunk-97-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

Switch Rate

plot_switch_rate <- function(df, m1, m2, pop, chrom = 15){
  p <- df %>%
    mutate(Beagle = n_other_beagle / n_hets,
         Eagle = n_other_eagle / n_hets,
         SHAPEIT = n_other_shapeit / n_hets) %>%
    ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
    geom_point() +
    geom_abline(slope = 1, intercept = 0) +
    ggtitle("Switch Rate", paste0("Chromosome ", chrom)) +
    theme_classic() +
    xlab(m1) +
    ylab(m2) +
    labs(color="Population") +
    scale_color_manual(values = cbPalette)
  return(p)
}

plot_switch_rate_noth <- function(df, m1, m2, pop, chrom = 15){
  p <- df %>%
    mutate(Beagle = n_switch_b / n_het,
         Eagle = n_switch_e / n_het,
         SHAPEIT = n_switch_s / n_het) %>%
    ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
    geom_point() +
    geom_abline(slope = 1, intercept = 0) +
    ggtitle("Switch Rate", paste0("Chromosome ", chrom)) +
    theme_classic() +
    xlab(m1) +
    ylab(m2) +
    labs(color="Population") +
    scale_color_manual(values = cbPalette)
  return(p)
}

Chromosome 1

chrom <- 1
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-99-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-99-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-99-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-99-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-99-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-99-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-99-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-99-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 2

chrom <- 2
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-100-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-100-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-100-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-100-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-100-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-100-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-100-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-100-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 3

chrom <- 3
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-101-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-101-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-101-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-101-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-101-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-101-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-101-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-101-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 4

chrom <- 4
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-102-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-102-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-102-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-102-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-102-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-102-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-102-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-102-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 5

chrom <- 5
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-103-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-103-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-103-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-103-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-103-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-103-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-103-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-103-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 6

chrom <- 6
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-104-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-104-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-104-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-104-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-104-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-104-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-104-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-104-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 7

chrom <- 7
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-105-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-105-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-105-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-105-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-105-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-105-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-105-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-105-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 8

chrom <- 8
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-106-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-106-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-106-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-106-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-106-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-106-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-106-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-106-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 9

chrom <- 9
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-107-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-107-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-107-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-107-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-107-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-107-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-107-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-107-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 10

chrom <- 10
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-108-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-108-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-108-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-108-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-108-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-108-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-108-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-108-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 11

chrom <- 11
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-109-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-109-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-109-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-109-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-109-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-109-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-109-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-109-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 12

chrom <- 12
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-110-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-110-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-110-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-110-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-110-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-110-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-110-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-110-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 13

chrom <- 13
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-111-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-111-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-111-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-111-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-111-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-111-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-111-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-111-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 14

chrom <- 14
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-112-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-112-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-112-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-112-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-112-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-112-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-112-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-112-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 15

chrom <- 15
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-113-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-113-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-113-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-113-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-113-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-113-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-113-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-113-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 16

chrom <- 16
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-114-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-114-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-114-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-114-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-114-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-114-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-114-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-114-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 17

chrom <- 17
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-115-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-115-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-115-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-115-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-115-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-115-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-115-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-115-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 18

chrom <- 18
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-116-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-116-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-116-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-116-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-116-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-116-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-116-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-116-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 19

chrom <- 19
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-117-1.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-117-2.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-117-3.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-117-4.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-117-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-117-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-117-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-117-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 20

chrom <- 20
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-118-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-118-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-118-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-118-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-118-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-118-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-118-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-118-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 21

chrom <- 21
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-119-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-119-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-119-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-119-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Chromosome 22

chrom <- 22
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-120-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-120-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-120-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-120-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

Chromosome X

plot_switch_rate(df_switch_x, "Beagle", "Eagle", "pop", "X")

Past versions of unnamed-chunk-121-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_x, "Beagle", "SHAPEIT", "pop", "X")

Past versions of unnamed-chunk-121-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_switch_rate(df_switch_x, "SHAPEIT", "Eagle", "pop", "X")

Past versions of unnamed-chunk-121-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

cross_meth_plot(df_switch_x, "Switches", plot_switch_rate, "pop", "X")

Past versions of unnamed-chunk-121-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

Flips

plot_flips <- function(df, m1, m2, pop, chrom = 15){
  p <- df %>%
    mutate(Beagle = n_flip_beagle,
         Eagle = n_flip_eagle,
         SHAPEIT = n_flip_shapeit) %>%
    ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
    geom_point() +
    geom_abline(slope = 1, intercept = 0) +
    ggtitle("Total Flips", paste0("Chromosome ", chrom)) +
    theme_classic() +
    xlab(m1) +
    ylab(m2) +
    labs(color="Population") +
    scale_color_manual(values = cbPalette)
  return(p)
}

plot_flips_noth <- function(df, m1, m2, pop, chrom = 15){
  p <- df %>%
    mutate(Beagle = n_flip_b,
         Eagle = n_flip_e,
         SHAPEIT = n_flip_s) %>%
    ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
    geom_point() +
    geom_abline(slope = 1, intercept = 0) +
    ggtitle("Total Flips", paste0("Chromosome ", chrom)) +
    theme_classic() +
    xlab(m1) +
    ylab(m2) +
    labs(color="Population") +
    scale_color_manual(values = cbPalette)
  return(p)
}

table_flip <- function(df, pop){
  res <- df %>%
    mutate(Beagle = (n_flip_beagle ),
         Eagle =  (n_flip_eagle),
         SHAPEIT =  (n_flip_shapeit)) %>%
    mutate(b_l_e = factor(Beagle < Eagle),
           b_l_s = factor(Beagle < SHAPEIT),
           e_l_b = factor(Beagle > Eagle),
           e_l_s = factor(Eagle < SHAPEIT),
           s_l_b = factor(SHAPEIT < Beagle),
           s_l_e = factor(SHAPEIT < Eagle)) %>%
    tbl_summary(by = !! sym(pop),  
                include = c(b_l_e, b_l_s, e_l_b, e_l_s, s_l_b, s_l_e))
    
  return(res)
}

table_flip_noth <- function(df, pop){
  res <- df %>%
    mutate(Beagle = (n_flip_b ),
         Eagle =  (n_flip_e),
         SHAPEIT =  (n_flip_s)) %>%
    mutate(b_l_e = factor(Beagle < Eagle),
           b_l_s = factor(Beagle < SHAPEIT),
           e_l_b = factor(Beagle > Eagle),
           e_l_s = factor(Eagle < SHAPEIT),
           s_l_b = factor(SHAPEIT < Beagle),
           s_l_e = factor(SHAPEIT < Eagle)) %>%
    tbl_summary(by = !! sym(pop),  
                include = c(b_l_e, b_l_s, e_l_b, e_l_s, s_l_b, s_l_e))
    
  return(res)
}

Chromosome 1

chrom <- 1
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-123-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-123-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-123-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-123-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-123-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-123-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_flip(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	134 (98%)	69 (96%)	107 (100%)	85 (100%)
TRUE	0 (0%)	3 (2.2%)	3 (4.2%)	0 (0%)	0 (0%)
b_l_s
FALSE	2 (1.0%)	2 (1.5%)	2 (2.8%)	0 (0%)	0 (0%)
TRUE	199 (99%)	135 (99%)	70 (97%)	107 (100%)	85 (100%)
e_l_b
FALSE	0 (0%)	3 (2.2%)	3 (4.2%)	0 (0%)	0 (0%)
TRUE	201 (100%)	134 (98%)	69 (96%)	107 (100%)	85 (100%)
e_l_s
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	199 (99%)	135 (99%)	70 (97%)	107 (100%)	85 (100%)
TRUE	2 (1.0%)	2 (1.5%)	2 (2.8%)	0 (0%)	0 (0%)
s_l_e
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
1 n (%)

table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	131 (96%)	70 (97%)	102 (95%)	85 (100%)
TRUE	0 (0%)	6 (4.4%)	2 (2.8%)	5 (4.7%)	0 (0%)
b_l_s
FALSE	2 (1.0%)	9 (6.6%)	4 (5.6%)	10 (9.3%)	1 (1.2%)
TRUE	199 (99%)	128 (93%)	68 (94%)	97 (91%)	84 (99%)
e_l_b
FALSE	0 (0%)	6 (4.4%)	2 (2.8%)	5 (4.7%)	0 (0%)
TRUE	201 (100%)	131 (96%)	70 (97%)	102 (95%)	85 (100%)
e_l_s
FALSE	0 (0%)	1 (0.7%)	0 (0%)	0 (0%)	0 (0%)
TRUE	201 (100%)	136 (99%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	199 (99%)	129 (94%)	68 (94%)	97 (91%)	85 (100%)
TRUE	2 (1.0%)	8 (5.8%)	4 (5.6%)	10 (9.3%)	0 (0%)
s_l_e
FALSE	201 (100%)	136 (99%)	72 (100%)	107 (100%)	85 (100%)
TRUE	0 (0%)	1 (0.7%)	0 (0%)	0 (0%)	0 (0%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-123-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-123-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 2

chrom <- 2
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-124-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-124-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-124-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-124-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-124-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-124-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_flip(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	128 (93%)	70 (97%)	105 (98%)	85 (100%)
TRUE	0 (0%)	9 (6.6%)	2 (2.8%)	2 (1.9%)	0 (0%)
b_l_s
FALSE	3 (1.5%)	7 (5.1%)	2 (2.8%)	8 (7.5%)	1 (1.2%)
TRUE	198 (99%)	130 (95%)	70 (97%)	99 (93%)	84 (99%)
e_l_b
FALSE	0 (0%)	9 (6.6%)	2 (2.8%)	2 (1.9%)	0 (0%)
TRUE	201 (100%)	128 (93%)	70 (97%)	105 (98%)	85 (100%)
e_l_s
FALSE	0 (0%)	2 (1.5%)	0 (0%)	0 (0%)	0 (0%)
TRUE	201 (100%)	135 (99%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	199 (99%)	132 (96%)	70 (97%)	100 (93%)	84 (99%)
TRUE	2 (1.0%)	5 (3.6%)	2 (2.8%)	7 (6.5%)	1 (1.2%)
s_l_e
FALSE	201 (100%)	135 (99%)	72 (100%)	107 (100%)	85 (100%)
TRUE	0 (0%)	2 (1.5%)	0 (0%)	0 (0%)	0 (0%)
1 n (%)

table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	134 (98%)	72 (100%)	106 (99%)	85 (100%)
TRUE	0 (0%)	3 (2.2%)	0 (0%)	1 (0.9%)	0 (0%)
b_l_s
FALSE	4 (2.0%)	5 (3.6%)	1 (1.4%)	2 (1.9%)	0 (0%)
TRUE	197 (98%)	132 (96%)	71 (99%)	105 (98%)	85 (100%)
e_l_b
FALSE	0 (0%)	4 (2.9%)	0 (0%)	1 (0.9%)	0 (0%)
TRUE	201 (100%)	133 (97%)	72 (100%)	106 (99%)	85 (100%)
e_l_s
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	197 (98%)	132 (96%)	71 (99%)	105 (98%)	85 (100%)
TRUE	4 (2.0%)	5 (3.6%)	1 (1.4%)	2 (1.9%)	0 (0%)
s_l_e
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-124-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-124-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 3

chrom <- 3
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-125-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-125-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-125-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-125-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-125-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-125-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_flip(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	131 (96%)	70 (97%)	104 (97%)	85 (100%)
TRUE	0 (0%)	6 (4.4%)	2 (2.8%)	3 (2.8%)	0 (0%)
b_l_s
FALSE	3 (1.5%)	7 (5.1%)	4 (5.6%)	4 (3.7%)	1 (1.2%)
TRUE	198 (99%)	130 (95%)	68 (94%)	103 (96%)	84 (99%)
e_l_b
FALSE	0 (0%)	7 (5.1%)	2 (2.8%)	3 (2.8%)	0 (0%)
TRUE	201 (100%)	130 (95%)	70 (97%)	104 (97%)	85 (100%)
e_l_s
FALSE	0 (0%)	1 (0.7%)	0 (0%)	0 (0%)	0 (0%)
TRUE	201 (100%)	136 (99%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	198 (99%)	130 (95%)	69 (96%)	104 (97%)	84 (99%)
TRUE	3 (1.5%)	7 (5.1%)	3 (4.2%)	3 (2.8%)	1 (1.2%)
s_l_e
FALSE	201 (100%)	136 (99%)	72 (100%)	107 (100%)	85 (100%)
TRUE	0 (0%)	1 (0.7%)	0 (0%)	0 (0%)	0 (0%)
1 n (%)

table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	200 (100%)	134 (98%)	71 (99%)	100 (93%)	84 (99%)
TRUE	1 (0.5%)	3 (2.2%)	1 (1.4%)	7 (6.5%)	1 (1.2%)
b_l_s
FALSE	4 (2.0%)	8 (5.8%)	6 (8.3%)	7 (6.5%)	1 (1.2%)
TRUE	197 (98%)	129 (94%)	66 (92%)	100 (93%)	84 (99%)
e_l_b
FALSE	1 (0.5%)	3 (2.2%)	1 (1.4%)	7 (6.5%)	1 (1.2%)
TRUE	200 (100%)	134 (98%)	71 (99%)	100 (93%)	84 (99%)
e_l_s
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	197 (98%)	129 (94%)	67 (93%)	101 (94%)	84 (99%)
TRUE	4 (2.0%)	8 (5.8%)	5 (6.9%)	6 (5.6%)	1 (1.2%)
s_l_e
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-125-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-125-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 4

chrom <- 4
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-126-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-126-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-126-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-126-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-126-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-126-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_flip(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	133 (97%)	71 (99%)	105 (98%)	85 (100%)
TRUE	0 (0%)	4 (2.9%)	1 (1.4%)	2 (1.9%)	0 (0%)
b_l_s
FALSE	8 (4.0%)	7 (5.1%)	1 (1.4%)	5 (4.7%)	0 (0%)
TRUE	193 (96%)	130 (95%)	71 (99%)	102 (95%)	85 (100%)
e_l_b
FALSE	0 (0%)	5 (3.6%)	1 (1.4%)	3 (2.8%)	0 (0%)
TRUE	201 (100%)	132 (96%)	71 (99%)	104 (97%)	85 (100%)
e_l_s
FALSE	0 (0%)	1 (0.7%)	0 (0%)	0 (0%)	0 (0%)
TRUE	201 (100%)	136 (99%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	193 (96%)	130 (95%)	71 (99%)	102 (95%)	85 (100%)
TRUE	8 (4.0%)	7 (5.1%)	1 (1.4%)	5 (4.7%)	0 (0%)
s_l_e
FALSE	201 (100%)	136 (99%)	72 (100%)	107 (100%)	85 (100%)
TRUE	0 (0%)	1 (0.7%)	0 (0%)	0 (0%)	0 (0%)
1 n (%)

table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	130 (95%)	68 (94%)	105 (98%)	85 (100%)
TRUE	0 (0%)	7 (5.1%)	4 (5.6%)	2 (1.9%)	0 (0%)
b_l_s
FALSE	10 (5.0%)	16 (12%)	4 (5.6%)	6 (5.6%)	3 (3.5%)
TRUE	191 (95%)	121 (88%)	68 (94%)	101 (94%)	82 (96%)
e_l_b
FALSE	0 (0%)	7 (5.1%)	5 (6.9%)	2 (1.9%)	0 (0%)
TRUE	201 (100%)	130 (95%)	67 (93%)	105 (98%)	85 (100%)
e_l_s
FALSE	0 (0%)	6 (4.4%)	0 (0%)	0 (0%)	0 (0%)
TRUE	201 (100%)	131 (96%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	192 (96%)	122 (89%)	69 (96%)	101 (94%)	83 (98%)
TRUE	9 (4.5%)	15 (11%)	3 (4.2%)	6 (5.6%)	2 (2.4%)
s_l_e
FALSE	201 (100%)	131 (96%)	72 (100%)	107 (100%)	85 (100%)
TRUE	0 (0%)	6 (4.4%)	0 (0%)	0 (0%)	0 (0%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-126-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-126-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 5

chrom <- 5
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-127-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-127-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-127-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-127-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-127-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-127-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_flip(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	127 (93%)	70 (97%)	105 (98%)	83 (98%)
TRUE	0 (0%)	10 (7.3%)	2 (2.8%)	2 (1.9%)	2 (2.4%)
b_l_s
FALSE	2 (1.0%)	7 (5.1%)	6 (8.3%)	5 (4.7%)	1 (1.2%)
TRUE	199 (99%)	130 (95%)	66 (92%)	102 (95%)	84 (99%)
e_l_b
FALSE	0 (0%)	10 (7.3%)	3 (4.2%)	2 (1.9%)	2 (2.4%)
TRUE	201 (100%)	127 (93%)	69 (96%)	105 (98%)	83 (98%)
e_l_s
FALSE	0 (0%)	1 (0.7%)	1 (1.4%)	0 (0%)	0 (0%)
TRUE	201 (100%)	136 (99%)	71 (99%)	107 (100%)	85 (100%)
s_l_b
FALSE	199 (99%)	131 (96%)	66 (92%)	102 (95%)	84 (99%)
TRUE	2 (1.0%)	6 (4.4%)	6 (8.3%)	5 (4.7%)	1 (1.2%)
s_l_e
FALSE	201 (100%)	136 (99%)	71 (99%)	107 (100%)	85 (100%)
TRUE	0 (0%)	1 (0.7%)	1 (1.4%)	0 (0%)	0 (0%)
1 n (%)

table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	129 (94%)	69 (96%)	105 (98%)	85 (100%)
TRUE	0 (0%)	8 (5.8%)	3 (4.2%)	2 (1.9%)	0 (0%)
b_l_s
FALSE	10 (5.0%)	9 (6.6%)	2 (2.8%)	6 (5.6%)	1 (1.2%)
TRUE	191 (95%)	128 (93%)	70 (97%)	101 (94%)	84 (99%)
e_l_b
FALSE	0 (0%)	8 (5.8%)	3 (4.2%)	2 (1.9%)	0 (0%)
TRUE	201 (100%)	129 (94%)	69 (96%)	105 (98%)	85 (100%)
e_l_s
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	191 (95%)	129 (94%)	70 (97%)	101 (94%)	84 (99%)
TRUE	10 (5.0%)	8 (5.8%)	2 (2.8%)	6 (5.6%)	1 (1.2%)
s_l_e
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-127-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-127-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 6

chrom <- 6
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-128-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-128-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-128-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-128-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-128-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-128-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_flip(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	118 (86%)	66 (92%)	98 (92%)	83 (98%)
TRUE	0 (0%)	19 (14%)	6 (8.3%)	9 (8.4%)	2 (2.4%)
b_l_s
FALSE	3 (1.5%)	9 (6.6%)	2 (2.8%)	7 (6.5%)	1 (1.2%)
TRUE	198 (99%)	128 (93%)	70 (97%)	100 (93%)	84 (99%)
e_l_b
FALSE	0 (0%)	19 (14%)	6 (8.3%)	9 (8.4%)	2 (2.4%)
TRUE	201 (100%)	118 (86%)	66 (92%)	98 (92%)	83 (98%)
e_l_s
FALSE	0 (0%)	7 (5.1%)	0 (0%)	1 (0.9%)	0 (0%)
TRUE	201 (100%)	130 (95%)	72 (100%)	106 (99%)	85 (100%)
s_l_b
FALSE	199 (99%)	128 (93%)	70 (97%)	102 (95%)	84 (99%)
TRUE	2 (1.0%)	9 (6.6%)	2 (2.8%)	5 (4.7%)	1 (1.2%)
s_l_e
FALSE	201 (100%)	131 (96%)	72 (100%)	106 (99%)	85 (100%)
TRUE	0 (0%)	6 (4.4%)	0 (0%)	1 (0.9%)	0 (0%)
1 n (%)

table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	127 (93%)	70 (97%)	105 (98%)	85 (100%)
TRUE	0 (0%)	10 (7.3%)	2 (2.8%)	2 (1.9%)	0 (0%)
b_l_s
FALSE	6 (3.0%)	12 (8.8%)	3 (4.2%)	8 (7.5%)	2 (2.4%)
TRUE	195 (97%)	125 (91%)	69 (96%)	99 (93%)	83 (98%)
e_l_b
FALSE	0 (0%)	10 (7.3%)	2 (2.8%)	4 (3.7%)	0 (0%)
TRUE	201 (100%)	127 (93%)	70 (97%)	103 (96%)	85 (100%)
e_l_s
FALSE	0 (0%)	3 (2.2%)	0 (0%)	0 (0%)	0 (0%)
TRUE	201 (100%)	134 (98%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	195 (97%)	127 (93%)	69 (96%)	100 (93%)	83 (98%)
TRUE	6 (3.0%)	10 (7.3%)	3 (4.2%)	7 (6.5%)	2 (2.4%)
s_l_e
FALSE	201 (100%)	134 (98%)	72 (100%)	107 (100%)	85 (100%)
TRUE	0 (0%)	3 (2.2%)	0 (0%)	0 (0%)	0 (0%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-128-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-128-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 7

chrom <- 7
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-129-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-129-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-129-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-129-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-129-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-129-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_flip(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	127 (93%)	69 (96%)	99 (93%)	84 (99%)
TRUE	0 (0%)	10 (7.3%)	3 (4.2%)	8 (7.5%)	1 (1.2%)
b_l_s
FALSE	6 (3.0%)	1 (0.7%)	3 (4.2%)	6 (5.6%)	1 (1.2%)
TRUE	195 (97%)	136 (99%)	69 (96%)	101 (94%)	84 (99%)
e_l_b
FALSE	0 (0%)	11 (8.0%)	3 (4.2%)	9 (8.4%)	1 (1.2%)
TRUE	201 (100%)	126 (92%)	69 (96%)	98 (92%)	84 (99%)
e_l_s
FALSE	0 (0%)	0 (0%)	0 (0%)	1 (0.9%)	0 (0%)
TRUE	201 (100%)	137 (100%)	72 (100%)	106 (99%)	85 (100%)
s_l_b
FALSE	195 (97%)	136 (99%)	69 (96%)	101 (94%)	84 (99%)
TRUE	6 (3.0%)	1 (0.7%)	3 (4.2%)	6 (5.6%)	1 (1.2%)
s_l_e
FALSE	201 (100%)	137 (100%)	72 (100%)	106 (99%)	85 (100%)
TRUE	0 (0%)	0 (0%)	0 (0%)	1 (0.9%)	0 (0%)
1 n (%)

table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	200 (100%)	133 (97%)	71 (99%)	105 (98%)	83 (98%)
TRUE	1 (0.5%)	4 (2.9%)	1 (1.4%)	2 (1.9%)	2 (2.4%)
b_l_s
FALSE	8 (4.0%)	13 (9.5%)	5 (6.9%)	6 (5.6%)	2 (2.4%)
TRUE	193 (96%)	124 (91%)	67 (93%)	101 (94%)	83 (98%)
e_l_b
FALSE	1 (0.5%)	4 (2.9%)	1 (1.4%)	2 (1.9%)	2 (2.4%)
TRUE	200 (100%)	133 (97%)	71 (99%)	105 (98%)	83 (98%)
e_l_s
FALSE	0 (0%)	3 (2.2%)	0 (0%)	0 (0%)	0 (0%)
TRUE	201 (100%)	134 (98%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	195 (97%)	124 (91%)	67 (93%)	101 (94%)	83 (98%)
TRUE	6 (3.0%)	13 (9.5%)	5 (6.9%)	6 (5.6%)	2 (2.4%)
s_l_e
FALSE	201 (100%)	134 (98%)	72 (100%)	107 (100%)	85 (100%)
TRUE	0 (0%)	3 (2.2%)	0 (0%)	0 (0%)	0 (0%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-129-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-129-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 8

chrom <- 8
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-130-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-130-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-130-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-130-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-130-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-130-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_flip(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	63 (31%)	35 (26%)	1 (1.4%)	20 (19%)	29 (34%)
TRUE	138 (69%)	102 (74%)	71 (99%)	87 (81%)	56 (66%)
b_l_s
FALSE	81 (40%)	44 (32%)	49 (68%)	41 (38%)	32 (38%)
TRUE	120 (60%)	93 (68%)	23 (32%)	66 (62%)	53 (62%)
e_l_b
FALSE	138 (69%)	102 (74%)	71 (99%)	87 (81%)	57 (67%)
TRUE	63 (31%)	35 (26%)	1 (1.4%)	20 (19%)	28 (33%)
e_l_s
FALSE	140 (70%)	100 (73%)	69 (96%)	87 (81%)	56 (66%)
TRUE	61 (30%)	37 (27%)	3 (4.2%)	20 (19%)	29 (34%)
s_l_b
FALSE	124 (62%)	96 (70%)	29 (40%)	68 (64%)	55 (65%)
TRUE	77 (38%)	41 (30%)	43 (60%)	39 (36%)	30 (35%)
s_l_e
FALSE	61 (30%)	37 (27%)	3 (4.2%)	20 (19%)	29 (34%)
TRUE	140 (70%)	100 (73%)	69 (96%)	87 (81%)	56 (66%)
1 n (%)

table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	126 (92%)	70 (97%)	100 (93%)	84 (99%)
TRUE	0 (0%)	11 (8.0%)	2 (2.8%)	7 (6.5%)	1 (1.2%)
b_l_s
FALSE	5 (2.5%)	11 (8.0%)	13 (18%)	14 (13%)	4 (4.7%)
TRUE	196 (98%)	126 (92%)	59 (82%)	93 (87%)	81 (95%)
e_l_b
FALSE	0 (0%)	11 (8.0%)	2 (2.8%)	7 (6.5%)	1 (1.2%)
TRUE	201 (100%)	126 (92%)	70 (97%)	100 (93%)	84 (99%)
e_l_s
FALSE	0 (0%)	5 (3.6%)	2 (2.8%)	2 (1.9%)	1 (1.2%)
TRUE	201 (100%)	132 (96%)	70 (97%)	105 (98%)	84 (99%)
s_l_b
FALSE	196 (98%)	126 (92%)	59 (82%)	93 (87%)	81 (95%)
TRUE	5 (2.5%)	11 (8.0%)	13 (18%)	14 (13%)	4 (4.7%)
s_l_e
FALSE	201 (100%)	132 (96%)	70 (97%)	105 (98%)	84 (99%)
TRUE	0 (0%)	5 (3.6%)	2 (2.8%)	2 (1.9%)	1 (1.2%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-130-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-130-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 9

chrom <- 9
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-131-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-131-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-131-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-131-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-131-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-131-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_flip(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	125 (91%)	68 (94%)	98 (92%)	84 (99%)
TRUE	0 (0%)	12 (8.8%)	4 (5.6%)	9 (8.4%)	1 (1.2%)
b_l_s
FALSE	11 (5.5%)	7 (5.1%)	4 (5.6%)	10 (9.3%)	4 (4.7%)
TRUE	190 (95%)	130 (95%)	68 (94%)	97 (91%)	81 (95%)
e_l_b
FALSE	0 (0%)	14 (10%)	4 (5.6%)	10 (9.3%)	1 (1.2%)
TRUE	201 (100%)	123 (90%)	68 (94%)	97 (91%)	84 (99%)
e_l_s
FALSE	0 (0%)	4 (2.9%)	1 (1.4%)	0 (0%)	0 (0%)
TRUE	201 (100%)	133 (97%)	71 (99%)	107 (100%)	85 (100%)
s_l_b
FALSE	191 (95%)	130 (95%)	68 (94%)	97 (91%)	82 (96%)
TRUE	10 (5.0%)	7 (5.1%)	4 (5.6%)	10 (9.3%)	3 (3.5%)
s_l_e
FALSE	201 (100%)	133 (97%)	71 (99%)	107 (100%)	85 (100%)
TRUE	0 (0%)	4 (2.9%)	1 (1.4%)	0 (0%)	0 (0%)
1 n (%)

table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	128 (93%)	71 (99%)	100 (93%)	85 (100%)
TRUE	0 (0%)	9 (6.6%)	1 (1.4%)	7 (6.5%)	0 (0%)
b_l_s
FALSE	8 (4.0%)	8 (5.8%)	4 (5.6%)	14 (13%)	3 (3.5%)
TRUE	193 (96%)	129 (94%)	68 (94%)	93 (87%)	82 (96%)
e_l_b
FALSE	0 (0%)	9 (6.6%)	1 (1.4%)	8 (7.5%)	0 (0%)
TRUE	201 (100%)	128 (93%)	71 (99%)	99 (93%)	85 (100%)
e_l_s
FALSE	0 (0%)	4 (2.9%)	0 (0%)	0 (0%)	0 (0%)
TRUE	201 (100%)	133 (97%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	193 (96%)	129 (94%)	68 (94%)	96 (90%)	82 (96%)
TRUE	8 (4.0%)	8 (5.8%)	4 (5.6%)	11 (10%)	3 (3.5%)
s_l_e
FALSE	201 (100%)	133 (97%)	72 (100%)	107 (100%)	85 (100%)
TRUE	0 (0%)	4 (2.9%)	0 (0%)	0 (0%)	0 (0%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-131-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-131-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 10

chrom <- 10
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-132-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-132-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-132-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-132-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-132-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-132-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_flip(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	131 (96%)	63 (88%)	102 (95%)	81 (95%)
TRUE	0 (0%)	6 (4.4%)	9 (13%)	5 (4.7%)	4 (4.7%)
b_l_s
FALSE	5 (2.5%)	6 (4.4%)	5 (6.9%)	11 (10%)	1 (1.2%)
TRUE	196 (98%)	131 (96%)	67 (93%)	96 (90%)	84 (99%)
e_l_b
FALSE	0 (0%)	6 (4.4%)	9 (13%)	7 (6.5%)	4 (4.7%)
TRUE	201 (100%)	131 (96%)	63 (88%)	100 (93%)	81 (95%)
e_l_s
FALSE	0 (0%)	1 (0.7%)	2 (2.8%)	0 (0%)	0 (0%)
TRUE	201 (100%)	136 (99%)	70 (97%)	107 (100%)	85 (100%)
s_l_b
FALSE	197 (98%)	131 (96%)	67 (93%)	97 (91%)	84 (99%)
TRUE	4 (2.0%)	6 (4.4%)	5 (6.9%)	10 (9.3%)	1 (1.2%)
s_l_e
FALSE	201 (100%)	136 (99%)	70 (97%)	107 (100%)	85 (100%)
TRUE	0 (0%)	1 (0.7%)	2 (2.8%)	0 (0%)	0 (0%)
1 n (%)

table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	130 (95%)	68 (94%)	103 (96%)	84 (99%)
TRUE	0 (0%)	7 (5.1%)	4 (5.6%)	4 (3.7%)	1 (1.2%)
b_l_s
FALSE	6 (3.0%)	18 (13%)	4 (5.6%)	12 (11%)	2 (2.4%)
TRUE	195 (97%)	119 (87%)	68 (94%)	95 (89%)	83 (98%)
e_l_b
FALSE	0 (0%)	8 (5.8%)	5 (6.9%)	4 (3.7%)	2 (2.4%)
TRUE	201 (100%)	129 (94%)	67 (93%)	103 (96%)	83 (98%)
e_l_s
FALSE	0 (0%)	1 (0.7%)	1 (1.4%)	0 (0%)	0 (0%)
TRUE	201 (100%)	136 (99%)	71 (99%)	107 (100%)	85 (100%)
s_l_b
FALSE	196 (98%)	120 (88%)	68 (94%)	96 (90%)	83 (98%)
TRUE	5 (2.5%)	17 (12%)	4 (5.6%)	11 (10%)	2 (2.4%)
s_l_e
FALSE	201 (100%)	136 (99%)	71 (99%)	107 (100%)	85 (100%)
TRUE	0 (0%)	1 (0.7%)	1 (1.4%)	0 (0%)	0 (0%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-132-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-132-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 11

chrom <- 11
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-133-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-133-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-133-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-133-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-133-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-133-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_flip(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	124 (91%)	68 (94%)	101 (94%)	84 (99%)
TRUE	0 (0%)	13 (9.5%)	4 (5.6%)	6 (5.6%)	1 (1.2%)
b_l_s
FALSE	8 (4.0%)	13 (9.5%)	8 (11%)	16 (15%)	2 (2.4%)
TRUE	193 (96%)	124 (91%)	64 (89%)	91 (85%)	83 (98%)
e_l_b
FALSE	0 (0%)	14 (10%)	5 (6.9%)	6 (5.6%)	1 (1.2%)
TRUE	201 (100%)	123 (90%)	67 (93%)	101 (94%)	84 (99%)
e_l_s
FALSE	0 (0%)	6 (4.4%)	0 (0%)	1 (0.9%)	0 (0%)
TRUE	201 (100%)	131 (96%)	72 (100%)	106 (99%)	85 (100%)
s_l_b
FALSE	195 (97%)	125 (91%)	66 (92%)	91 (85%)	83 (98%)
TRUE	6 (3.0%)	12 (8.8%)	6 (8.3%)	16 (15%)	2 (2.4%)
s_l_e
FALSE	201 (100%)	132 (96%)	72 (100%)	106 (99%)	85 (100%)
TRUE	0 (0%)	5 (3.6%)	0 (0%)	1 (0.9%)	0 (0%)
1 n (%)

table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	125 (91%)	71 (99%)	101 (94%)	85 (100%)
TRUE	0 (0%)	12 (8.8%)	1 (1.4%)	6 (5.6%)	0 (0%)
b_l_s
FALSE	4 (2.0%)	13 (9.5%)	4 (5.6%)	9 (8.4%)	2 (2.4%)
TRUE	197 (98%)	124 (91%)	68 (94%)	98 (92%)	83 (98%)
e_l_b
FALSE	0 (0%)	12 (8.8%)	1 (1.4%)	6 (5.6%)	0 (0%)
TRUE	201 (100%)	125 (91%)	71 (99%)	101 (94%)	85 (100%)
e_l_s
FALSE	0 (0%)	5 (3.6%)	1 (1.4%)	0 (0%)	0 (0%)
TRUE	201 (100%)	132 (96%)	71 (99%)	107 (100%)	85 (100%)
s_l_b
FALSE	197 (98%)	124 (91%)	68 (94%)	99 (93%)	84 (99%)
TRUE	4 (2.0%)	13 (9.5%)	4 (5.6%)	8 (7.5%)	1 (1.2%)
s_l_e
FALSE	201 (100%)	133 (97%)	71 (99%)	107 (100%)	85 (100%)
TRUE	0 (0%)	4 (2.9%)	1 (1.4%)	0 (0%)	0 (0%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-133-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-133-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 12

chrom <- 12
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-134-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-134-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-134-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-134-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-134-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-134-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_flip(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	126 (92%)	67 (93%)	103 (96%)	83 (98%)
TRUE	0 (0%)	11 (8.0%)	5 (6.9%)	4 (3.7%)	2 (2.4%)
b_l_s
FALSE	13 (6.5%)	13 (9.5%)	6 (8.3%)	7 (6.5%)	4 (4.7%)
TRUE	188 (94%)	124 (91%)	66 (92%)	100 (93%)	81 (95%)
e_l_b
FALSE	0 (0%)	12 (8.8%)	5 (6.9%)	4 (3.7%)	2 (2.4%)
TRUE	201 (100%)	125 (91%)	67 (93%)	103 (96%)	83 (98%)
e_l_s
TRUE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	188 (94%)	125 (91%)	68 (94%)	101 (94%)	82 (96%)
TRUE	13 (6.5%)	12 (8.8%)	4 (5.6%)	6 (5.6%)	3 (3.5%)
s_l_e
FALSE	201 (100%)	137 (100%)	72 (100%)	107 (100%)	85 (100%)
1 n (%)

table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	131 (96%)	69 (96%)	104 (97%)	83 (98%)
TRUE	0 (0%)	6 (4.4%)	3 (4.2%)	3 (2.8%)	2 (2.4%)
b_l_s
FALSE	3 (1.5%)	13 (9.5%)	8 (11%)	9 (8.4%)	1 (1.2%)
TRUE	198 (99%)	124 (91%)	64 (89%)	98 (92%)	84 (99%)
e_l_b
FALSE	0 (0%)	6 (4.4%)	3 (4.2%)	3 (2.8%)	2 (2.4%)
TRUE	201 (100%)	131 (96%)	69 (96%)	104 (97%)	83 (98%)
e_l_s
FALSE	0 (0%)	2 (1.5%)	0 (0%)	0 (0%)	0 (0%)
TRUE	201 (100%)	135 (99%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	198 (99%)	125 (91%)	64 (89%)	99 (93%)	84 (99%)
TRUE	3 (1.5%)	12 (8.8%)	8 (11%)	8 (7.5%)	1 (1.2%)
s_l_e
FALSE	201 (100%)	135 (99%)	72 (100%)	107 (100%)	85 (100%)
TRUE	0 (0%)	2 (1.5%)	0 (0%)	0 (0%)	0 (0%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-134-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-134-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 13

chrom <- 13
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-135-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-135-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-135-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-135-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-135-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-135-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_flip(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	200 (100%)	121 (88%)	69 (96%)	101 (94%)	84 (99%)
TRUE	1 (0.5%)	16 (12%)	3 (4.2%)	6 (5.6%)	1 (1.2%)
b_l_s
FALSE	14 (7.0%)	11 (8.0%)	9 (13%)	11 (10%)	4 (4.7%)
TRUE	187 (93%)	126 (92%)	63 (88%)	96 (90%)	81 (95%)
e_l_b
FALSE	1 (0.5%)	18 (13%)	4 (5.6%)	6 (5.6%)	1 (1.2%)
TRUE	200 (100%)	119 (87%)	68 (94%)	101 (94%)	84 (99%)
e_l_s
FALSE	0 (0%)	4 (2.9%)	2 (2.8%)	0 (0%)	1 (1.2%)
TRUE	201 (100%)	133 (97%)	70 (97%)	107 (100%)	84 (99%)
s_l_b
FALSE	187 (93%)	127 (93%)	63 (88%)	98 (92%)	83 (98%)
TRUE	14 (7.0%)	10 (7.3%)	9 (13%)	9 (8.4%)	2 (2.4%)
s_l_e
FALSE	201 (100%)	133 (97%)	70 (97%)	107 (100%)	84 (99%)
TRUE	0 (0%)	4 (2.9%)	2 (2.8%)	0 (0%)	1 (1.2%)
1 n (%)

table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	200 (100%)	129 (94%)	68 (94%)	96 (90%)	76 (89%)
TRUE	1 (0.5%)	8 (5.8%)	4 (5.6%)	11 (10%)	9 (11%)
b_l_s
FALSE	11 (5.5%)	11 (8.0%)	9 (13%)	18 (17%)	5 (5.9%)
TRUE	190 (95%)	126 (92%)	63 (88%)	89 (83%)	80 (94%)
e_l_b
FALSE	1 (0.5%)	9 (6.6%)	4 (5.6%)	11 (10%)	9 (11%)
TRUE	200 (100%)	128 (93%)	68 (94%)	96 (90%)	76 (89%)
e_l_s
FALSE	0 (0%)	4 (2.9%)	1 (1.4%)	1 (0.9%)	1 (1.2%)
TRUE	201 (100%)	133 (97%)	71 (99%)	106 (99%)	84 (99%)
s_l_b
FALSE	190 (95%)	127 (93%)	64 (89%)	90 (84%)	80 (94%)
TRUE	11 (5.5%)	10 (7.3%)	8 (11%)	17 (16%)	5 (5.9%)
s_l_e
FALSE	201 (100%)	134 (98%)	72 (100%)	106 (99%)	84 (99%)
TRUE	0 (0%)	3 (2.2%)	0 (0%)	1 (0.9%)	1 (1.2%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-135-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-135-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 14

chrom <- 14
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-136-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-136-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-136-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-136-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-136-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-136-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_flip(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	200 (100%)	115 (84%)	59 (82%)	90 (84%)	82 (96%)
TRUE	1 (0.5%)	22 (16%)	13 (18%)	17 (16%)	3 (3.5%)
b_l_s
FALSE	9 (4.5%)	16 (12%)	8 (11%)	16 (15%)	6 (7.1%)
TRUE	192 (96%)	121 (88%)	64 (89%)	91 (85%)	79 (93%)
e_l_b
FALSE	1 (0.5%)	22 (16%)	13 (18%)	18 (17%)	4 (4.7%)
TRUE	200 (100%)	115 (84%)	59 (82%)	89 (83%)	81 (95%)
e_l_s
FALSE	0 (0%)	3 (2.2%)	1 (1.4%)	4 (3.7%)	0 (0%)
TRUE	201 (100%)	134 (98%)	71 (99%)	103 (96%)	85 (100%)
s_l_b
FALSE	193 (96%)	122 (89%)	64 (89%)	91 (85%)	79 (93%)
TRUE	8 (4.0%)	15 (11%)	8 (11%)	16 (15%)	6 (7.1%)
s_l_e
FALSE	201 (100%)	134 (98%)	71 (99%)	103 (96%)	85 (100%)
TRUE	0 (0%)	3 (2.2%)	1 (1.4%)	4 (3.7%)	0 (0%)
1 n (%)

table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	122 (89%)	64 (89%)	98 (92%)	83 (98%)
TRUE	0 (0%)	15 (11%)	8 (11%)	9 (8.4%)	2 (2.4%)
b_l_s
FALSE	7 (3.5%)	12 (8.8%)	9 (13%)	13 (12%)	5 (5.9%)
TRUE	194 (97%)	125 (91%)	63 (88%)	94 (88%)	80 (94%)
e_l_b
FALSE	0 (0%)	16 (12%)	8 (11%)	12 (11%)	2 (2.4%)
TRUE	201 (100%)	121 (88%)	64 (89%)	95 (89%)	83 (98%)
e_l_s
FALSE	0 (0%)	2 (1.5%)	1 (1.4%)	1 (0.9%)	0 (0%)
TRUE	201 (100%)	135 (99%)	71 (99%)	106 (99%)	85 (100%)
s_l_b
FALSE	194 (97%)	125 (91%)	63 (88%)	96 (90%)	80 (94%)
TRUE	7 (3.5%)	12 (8.8%)	9 (13%)	11 (10%)	5 (5.9%)
s_l_e
FALSE	201 (100%)	135 (99%)	71 (99%)	106 (99%)	85 (100%)
TRUE	0 (0%)	2 (1.5%)	1 (1.4%)	1 (0.9%)	0 (0%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-136-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-136-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 15

chrom <- 15
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-137-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-137-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-137-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-137-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-137-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-137-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_flip(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	194 (97%)	122 (89%)	65 (90%)	90 (84%)	81 (95%)
TRUE	7 (3.5%)	15 (11%)	7 (9.7%)	17 (16%)	4 (4.7%)
b_l_s
FALSE	11 (5.5%)	14 (10%)	8 (11%)	19 (18%)	3 (3.5%)
TRUE	190 (95%)	123 (90%)	64 (89%)	88 (82%)	82 (96%)
e_l_b
FALSE	7 (3.5%)	17 (12%)	8 (11%)	18 (17%)	5 (5.9%)
TRUE	194 (97%)	120 (88%)	64 (89%)	89 (83%)	80 (94%)
e_l_s
FALSE	0 (0%)	5 (3.6%)	0 (0%)	3 (2.8%)	0 (0%)
TRUE	201 (100%)	132 (96%)	72 (100%)	104 (97%)	85 (100%)
s_l_b
FALSE	192 (96%)	124 (91%)	67 (93%)	90 (84%)	83 (98%)
TRUE	9 (4.5%)	13 (9.5%)	5 (6.9%)	17 (16%)	2 (2.4%)
s_l_e
FALSE	201 (100%)	133 (97%)	72 (100%)	105 (98%)	85 (100%)
TRUE	0 (0%)	4 (2.9%)	0 (0%)	2 (1.9%)	0 (0%)
1 n (%)

table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	196 (98%)	129 (94%)	66 (92%)	100 (93%)	80 (94%)
TRUE	5 (2.5%)	8 (5.8%)	6 (8.3%)	7 (6.5%)	5 (5.9%)
b_l_s
FALSE	12 (6.0%)	15 (11%)	8 (11%)	21 (20%)	0 (0%)
TRUE	189 (94%)	122 (89%)	64 (89%)	86 (80%)	85 (100%)
e_l_b
FALSE	5 (2.5%)	12 (8.8%)	7 (9.7%)	8 (7.5%)	5 (5.9%)
TRUE	196 (98%)	125 (91%)	65 (90%)	99 (93%)	80 (94%)
e_l_s
FALSE	2 (1.0%)	4 (2.9%)	0 (0%)	3 (2.8%)	0 (0%)
TRUE	199 (99%)	133 (97%)	72 (100%)	104 (97%)	85 (100%)
s_l_b
FALSE	191 (95%)	125 (91%)	64 (89%)	87 (81%)	85 (100%)
TRUE	10 (5.0%)	12 (8.8%)	8 (11%)	20 (19%)	0 (0%)
s_l_e
FALSE	200 (100%)	133 (97%)	72 (100%)	104 (97%)	85 (100%)
TRUE	1 (0.5%)	4 (2.9%)	0 (0%)	3 (2.8%)	0 (0%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-137-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-137-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 16

chrom <- 16
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-138-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-138-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-138-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-138-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-138-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-138-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_flip(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	128 (93%)	68 (94%)	100 (93%)	85 (100%)
TRUE	0 (0%)	9 (6.6%)	4 (5.6%)	7 (6.5%)	0 (0%)
b_l_s
FALSE	6 (3.0%)	13 (9.5%)	7 (9.7%)	8 (7.5%)	4 (4.7%)
TRUE	195 (97%)	124 (91%)	65 (90%)	99 (93%)	81 (95%)
e_l_b
FALSE	0 (0%)	10 (7.3%)	5 (6.9%)	7 (6.5%)	0 (0%)
TRUE	201 (100%)	127 (93%)	67 (93%)	100 (93%)	85 (100%)
e_l_s
FALSE	0 (0%)	2 (1.5%)	0 (0%)	1 (0.9%)	0 (0%)
TRUE	201 (100%)	135 (99%)	72 (100%)	106 (99%)	85 (100%)
s_l_b
FALSE	195 (97%)	124 (91%)	66 (92%)	99 (93%)	81 (95%)
TRUE	6 (3.0%)	13 (9.5%)	6 (8.3%)	8 (7.5%)	4 (4.7%)
s_l_e
FALSE	201 (100%)	135 (99%)	72 (100%)	106 (99%)	85 (100%)
TRUE	0 (0%)	2 (1.5%)	0 (0%)	1 (0.9%)	0 (0%)
1 n (%)

table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	128 (93%)	70 (97%)	92 (86%)	82 (96%)
TRUE	0 (0%)	9 (6.6%)	2 (2.8%)	15 (14%)	3 (3.5%)
b_l_s
FALSE	10 (5.0%)	13 (9.5%)	15 (21%)	12 (11%)	9 (11%)
TRUE	191 (95%)	124 (91%)	57 (79%)	95 (89%)	76 (89%)
e_l_b
FALSE	0 (0%)	9 (6.6%)	2 (2.8%)	16 (15%)	3 (3.5%)
TRUE	201 (100%)	128 (93%)	70 (97%)	91 (85%)	82 (96%)
e_l_s
FALSE	3 (1.5%)	1 (0.7%)	1 (1.4%)	1 (0.9%)	2 (2.4%)
TRUE	198 (99%)	136 (99%)	71 (99%)	106 (99%)	83 (98%)
s_l_b
FALSE	192 (96%)	126 (92%)	59 (82%)	96 (90%)	76 (89%)
TRUE	9 (4.5%)	11 (8.0%)	13 (18%)	11 (10%)	9 (11%)
s_l_e
FALSE	198 (99%)	137 (100%)	71 (99%)	106 (99%)	83 (98%)
TRUE	3 (1.5%)	0 (0%)	1 (1.4%)	1 (0.9%)	2 (2.4%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-138-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-138-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 17

chrom <- 17
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-139-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-139-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-139-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-139-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-139-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-139-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_flip(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	200 (100%)	125 (91%)	66 (92%)	89 (83%)	79 (93%)
TRUE	1 (0.5%)	12 (8.8%)	6 (8.3%)	18 (17%)	6 (7.1%)
b_l_s
FALSE	10 (5.0%)	15 (11%)	9 (13%)	18 (17%)	5 (5.9%)
TRUE	191 (95%)	122 (89%)	63 (88%)	89 (83%)	80 (94%)
e_l_b
FALSE	2 (1.0%)	14 (10%)	6 (8.3%)	21 (20%)	6 (7.1%)
TRUE	199 (99%)	123 (90%)	66 (92%)	86 (80%)	79 (93%)
e_l_s
FALSE	0 (0%)	3 (2.2%)	0 (0%)	0 (0%)	0 (0%)
TRUE	201 (100%)	134 (98%)	72 (100%)	107 (100%)	85 (100%)
s_l_b
FALSE	192 (96%)	122 (89%)	63 (88%)	90 (84%)	81 (95%)
TRUE	9 (4.5%)	15 (11%)	9 (13%)	17 (16%)	4 (4.7%)
s_l_e
FALSE	201 (100%)	134 (98%)	72 (100%)	107 (100%)	85 (100%)
TRUE	0 (0%)	3 (2.2%)	0 (0%)	0 (0%)	0 (0%)
1 n (%)

table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	183 (91%)	128 (93%)	67 (93%)	99 (93%)	82 (96%)
TRUE	18 (9.0%)	9 (6.6%)	5 (6.9%)	8 (7.5%)	3 (3.5%)
b_l_s
FALSE	14 (7.0%)	12 (8.8%)	13 (18%)	20 (19%)	5 (5.9%)
TRUE	187 (93%)	125 (91%)	59 (82%)	87 (81%)	80 (94%)
e_l_b
FALSE	18 (9.0%)	9 (6.6%)	5 (6.9%)	8 (7.5%)	3 (3.5%)
TRUE	183 (91%)	128 (93%)	67 (93%)	99 (93%)	82 (96%)
e_l_s
FALSE	0 (0%)	2 (1.5%)	1 (1.4%)	1 (0.9%)	0 (0%)
TRUE	201 (100%)	135 (99%)	71 (99%)	106 (99%)	85 (100%)
s_l_b
FALSE	189 (94%)	125 (91%)	59 (82%)	91 (85%)	80 (94%)
TRUE	12 (6.0%)	12 (8.8%)	13 (18%)	16 (15%)	5 (5.9%)
s_l_e
FALSE	201 (100%)	136 (99%)	71 (99%)	106 (99%)	85 (100%)
TRUE	0 (0%)	1 (0.7%)	1 (1.4%)	1 (0.9%)	0 (0%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-139-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-139-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 18

chrom <- 18
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-140-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-140-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-140-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-140-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-140-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-140-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_flip(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	200 (100%)	120 (88%)	64 (89%)	93 (87%)	78 (92%)
TRUE	1 (0.5%)	17 (12%)	8 (11%)	14 (13%)	7 (8.2%)
b_l_s
FALSE	16 (8.0%)	17 (12%)	9 (13%)	22 (21%)	3 (3.5%)
TRUE	185 (92%)	120 (88%)	63 (88%)	85 (79%)	82 (96%)
e_l_b
FALSE	1 (0.5%)	17 (12%)	8 (11%)	14 (13%)	7 (8.2%)
TRUE	200 (100%)	120 (88%)	64 (89%)	93 (87%)	78 (92%)
e_l_s
FALSE	0 (0%)	3 (2.2%)	3 (4.2%)	3 (2.8%)	0 (0%)
TRUE	201 (100%)	134 (98%)	69 (96%)	104 (97%)	85 (100%)
s_l_b
FALSE	185 (92%)	120 (88%)	63 (88%)	87 (81%)	83 (98%)
TRUE	16 (8.0%)	17 (12%)	9 (13%)	20 (19%)	2 (2.4%)
s_l_e
FALSE	201 (100%)	134 (98%)	69 (96%)	104 (97%)	85 (100%)
TRUE	0 (0%)	3 (2.2%)	3 (4.2%)	3 (2.8%)	0 (0%)
1 n (%)

table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	199 (99%)	126 (92%)	68 (94%)	95 (89%)	81 (95%)
TRUE	2 (1.0%)	11 (8.0%)	4 (5.6%)	12 (11%)	4 (4.7%)
b_l_s
FALSE	6 (3.0%)	14 (10%)	11 (15%)	19 (18%)	9 (11%)
TRUE	195 (97%)	123 (90%)	61 (85%)	88 (82%)	76 (89%)
e_l_b
FALSE	2 (1.0%)	12 (8.8%)	5 (6.9%)	14 (13%)	4 (4.7%)
TRUE	199 (99%)	125 (91%)	67 (93%)	93 (87%)	81 (95%)
e_l_s
FALSE	0 (0%)	0 (0%)	1 (1.4%)	1 (0.9%)	1 (1.2%)
TRUE	201 (100%)	137 (100%)	71 (99%)	106 (99%)	84 (99%)
s_l_b
FALSE	195 (97%)	125 (91%)	62 (86%)	88 (82%)	76 (89%)
TRUE	6 (3.0%)	12 (8.8%)	10 (14%)	19 (18%)	9 (11%)
s_l_e
FALSE	201 (100%)	137 (100%)	71 (99%)	106 (99%)	84 (99%)
TRUE	0 (0%)	0 (0%)	1 (1.4%)	1 (0.9%)	1 (1.2%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-140-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-140-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 19

chrom <- 19
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-141-1.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-141-2.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-141-3.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-141-4.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-141-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-141-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_flip(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	199 (99%)	113 (82%)	61 (85%)	93 (87%)	82 (96%)
TRUE	2 (1.0%)	24 (18%)	11 (15%)	14 (13%)	3 (3.5%)
b_l_s
FALSE	20 (10.0%)	12 (8.8%)	12 (17%)	23 (21%)	5 (5.9%)
TRUE	181 (90%)	125 (91%)	60 (83%)	84 (79%)	80 (94%)
e_l_b
FALSE	2 (1.0%)	25 (18%)	11 (15%)	16 (15%)	4 (4.7%)
TRUE	199 (99%)	112 (82%)	61 (85%)	91 (85%)	81 (95%)
e_l_s
FALSE	0 (0%)	4 (2.9%)	3 (4.2%)	5 (4.7%)	0 (0%)
TRUE	201 (100%)	133 (97%)	69 (96%)	102 (95%)	85 (100%)
s_l_b
FALSE	182 (91%)	127 (93%)	62 (86%)	86 (80%)	80 (94%)
TRUE	19 (9.5%)	10 (7.3%)	10 (14%)	21 (20%)	5 (5.9%)
s_l_e
FALSE	201 (100%)	133 (97%)	69 (96%)	103 (96%)	85 (100%)
TRUE	0 (0%)	4 (2.9%)	3 (4.2%)	4 (3.7%)	0 (0%)
1 n (%)

table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	198 (99%)	127 (93%)	64 (89%)	93 (87%)	81 (95%)
TRUE	3 (1.5%)	10 (7.3%)	8 (11%)	14 (13%)	4 (4.7%)
b_l_s
FALSE	22 (11%)	17 (12%)	15 (21%)	24 (22%)	5 (5.9%)
TRUE	179 (89%)	120 (88%)	57 (79%)	83 (78%)	80 (94%)
e_l_b
FALSE	3 (1.5%)	12 (8.8%)	9 (13%)	14 (13%)	4 (4.7%)
TRUE	198 (99%)	125 (91%)	63 (88%)	93 (87%)	81 (95%)
e_l_s
FALSE	0 (0%)	4 (2.9%)	2 (2.8%)	4 (3.7%)	0 (0%)
TRUE	201 (100%)	133 (97%)	70 (97%)	103 (96%)	85 (100%)
s_l_b
FALSE	180 (90%)	123 (90%)	58 (81%)	85 (79%)	82 (96%)
TRUE	21 (10%)	14 (10%)	14 (19%)	22 (21%)	3 (3.5%)
s_l_e
FALSE	201 (100%)	133 (97%)	70 (97%)	104 (97%)	85 (100%)
TRUE	0 (0%)	4 (2.9%)	2 (2.8%)	3 (2.8%)	0 (0%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-141-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-141-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 20

chrom <- 20
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-142-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-142-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-142-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-142-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-142-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-142-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

table_flip(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	201 (100%)	126 (92%)	62 (86%)	91 (85%)	81 (95%)
TRUE	0 (0%)	11 (8.0%)	10 (14%)	16 (15%)	4 (4.7%)
b_l_s
FALSE	28 (14%)	23 (17%)	8 (11%)	10 (9.3%)	12 (14%)
TRUE	173 (86%)	114 (83%)	64 (89%)	97 (91%)	73 (86%)
e_l_b
FALSE	0 (0%)	11 (8.0%)	12 (17%)	17 (16%)	4 (4.7%)
TRUE	201 (100%)	126 (92%)	60 (83%)	90 (84%)	81 (95%)
e_l_s
FALSE	0 (0%)	6 (4.4%)	1 (1.4%)	2 (1.9%)	0 (0%)
TRUE	201 (100%)	131 (96%)	71 (99%)	105 (98%)	85 (100%)
s_l_b
FALSE	175 (87%)	114 (83%)	64 (89%)	98 (92%)	74 (87%)
TRUE	26 (13%)	23 (17%)	8 (11%)	9 (8.4%)	11 (13%)
s_l_e
FALSE	201 (100%)	131 (96%)	71 (99%)	105 (98%)	85 (100%)
TRUE	0 (0%)	6 (4.4%)	1 (1.4%)	2 (1.9%)	0 (0%)
1 n (%)

table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	198 (99%)	121 (88%)	62 (86%)	89 (83%)	84 (99%)
TRUE	3 (1.5%)	16 (12%)	10 (14%)	18 (17%)	1 (1.2%)
b_l_s
FALSE	24 (12%)	21 (15%)	8 (11%)	20 (19%)	7 (8.2%)
TRUE	177 (88%)	116 (85%)	64 (89%)	87 (81%)	78 (92%)
e_l_b
FALSE	3 (1.5%)	16 (12%)	10 (14%)	19 (18%)	2 (2.4%)
TRUE	198 (99%)	121 (88%)	62 (86%)	88 (82%)	83 (98%)
e_l_s
FALSE	0 (0%)	4 (2.9%)	2 (2.8%)	4 (3.7%)	0 (0%)
TRUE	201 (100%)	133 (97%)	70 (97%)	103 (96%)	85 (100%)
s_l_b
FALSE	179 (89%)	117 (85%)	64 (89%)	88 (82%)	78 (92%)
TRUE	22 (11%)	20 (15%)	8 (11%)	19 (18%)	7 (8.2%)
s_l_e
FALSE	201 (100%)	134 (98%)	70 (97%)	103 (96%)	85 (100%)
TRUE	0 (0%)	3 (2.2%)	2 (2.8%)	4 (3.7%)	0 (0%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-142-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-142-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 21

chrom <- 21
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-143-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-143-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-143-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-143-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

table_flip(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	187 (93%)	97 (71%)	56 (78%)	76 (71%)	69 (81%)
TRUE	14 (7.0%)	40 (29%)	16 (22%)	31 (29%)	16 (19%)
b_l_s
FALSE	26 (13%)	19 (14%)	17 (24%)	19 (18%)	8 (9.4%)
TRUE	175 (87%)	118 (86%)	55 (76%)	88 (82%)	77 (91%)
e_l_b
FALSE	15 (7.5%)	43 (31%)	19 (26%)	32 (30%)	17 (20%)
TRUE	186 (93%)	94 (69%)	53 (74%)	75 (70%)	68 (80%)
e_l_s
FALSE	4 (2.0%)	13 (9.5%)	9 (13%)	13 (12%)	1 (1.2%)
TRUE	197 (98%)	124 (91%)	63 (88%)	94 (88%)	84 (99%)
s_l_b
FALSE	177 (88%)	122 (89%)	55 (76%)	92 (86%)	77 (91%)
TRUE	24 (12%)	15 (11%)	17 (24%)	15 (14%)	8 (9.4%)
s_l_e
FALSE	198 (99%)	125 (91%)	65 (90%)	95 (89%)	85 (100%)
TRUE	3 (1.5%)	12 (8.8%)	7 (9.7%)	12 (11%)	0 (0%)
1 n (%)

table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	193 (96%)	105 (77%)	60 (83%)	84 (79%)	73 (86%)
TRUE	8 (4.0%)	32 (23%)	12 (17%)	23 (21%)	12 (14%)
b_l_s
FALSE	29 (14%)	24 (18%)	17 (24%)	20 (19%)	13 (15%)
TRUE	172 (86%)	113 (82%)	55 (76%)	87 (81%)	72 (85%)
e_l_b
FALSE	10 (5.0%)	37 (27%)	12 (17%)	26 (24%)	13 (15%)
TRUE	191 (95%)	100 (73%)	60 (83%)	81 (76%)	72 (85%)
e_l_s
FALSE	1 (0.5%)	16 (12%)	3 (4.2%)	5 (4.7%)	3 (3.5%)
TRUE	200 (100%)	121 (88%)	69 (96%)	102 (95%)	82 (96%)
s_l_b
FALSE	178 (89%)	113 (82%)	57 (79%)	87 (81%)	73 (86%)
TRUE	23 (11%)	24 (18%)	15 (21%)	20 (19%)	12 (14%)
s_l_e
FALSE	200 (100%)	122 (89%)	69 (96%)	102 (95%)	82 (96%)
TRUE	1 (0.5%)	15 (11%)	3 (4.2%)	5 (4.7%)	3 (3.5%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Chromosome 22

chrom <- 22
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-144-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-144-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-144-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-144-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

table_flip(df_switch_trio[[chrom]], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	184 (92%)	109 (80%)	48 (67%)	76 (71%)	65 (76%)
TRUE	17 (8.5%)	28 (20%)	24 (33%)	31 (29%)	20 (24%)
b_l_s
FALSE	27 (13%)	21 (15%)	15 (21%)	18 (17%)	17 (20%)
TRUE	174 (87%)	116 (85%)	57 (79%)	89 (83%)	68 (80%)
e_l_b
FALSE	18 (9.0%)	34 (25%)	25 (35%)	37 (35%)	22 (26%)
TRUE	183 (91%)	103 (75%)	47 (65%)	70 (65%)	63 (74%)
e_l_s
FALSE	2 (1.0%)	18 (13%)	5 (6.9%)	12 (11%)	3 (3.5%)
TRUE	199 (99%)	119 (87%)	67 (93%)	95 (89%)	82 (96%)
s_l_b
FALSE	178 (89%)	117 (85%)	59 (82%)	91 (85%)	68 (80%)
TRUE	23 (11%)	20 (15%)	13 (18%)	16 (15%)	17 (20%)
s_l_e
FALSE	199 (99%)	124 (91%)	67 (93%)	96 (90%)	82 (96%)
TRUE	2 (1.0%)	13 (9.5%)	5 (6.9%)	11 (10%)	3 (3.5%)
1 n (%)

table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")

Characteristic	AFR N = 2011	AMR N = 1371	EAS N = 721	EUR N = 1071	SAS N = 851
b_l_e
FALSE	190 (95%)	108 (79%)	59 (82%)	81 (76%)	72 (85%)
TRUE	11 (5.5%)	29 (21%)	13 (18%)	26 (24%)	13 (15%)
b_l_s
FALSE	25 (12%)	20 (15%)	16 (22%)	20 (19%)	9 (11%)
TRUE	176 (88%)	117 (85%)	56 (78%)	87 (81%)	76 (89%)
e_l_b
FALSE	14 (7.0%)	31 (23%)	16 (22%)	30 (28%)	15 (18%)
TRUE	187 (93%)	106 (77%)	56 (78%)	77 (72%)	70 (82%)
e_l_s
FALSE	1 (0.5%)	16 (12%)	6 (8.3%)	10 (9.3%)	2 (2.4%)
TRUE	200 (100%)	121 (88%)	66 (92%)	97 (91%)	83 (98%)
s_l_b
FALSE	178 (89%)	119 (87%)	56 (78%)	89 (83%)	76 (89%)
TRUE	23 (11%)	18 (13%)	16 (22%)	18 (17%)	9 (11%)
s_l_e
FALSE	200 (100%)	122 (89%)	66 (92%)	100 (93%)	84 (99%)
TRUE	1 (0.5%)	15 (11%)	6 (8.3%)	7 (6.5%)	1 (1.2%)
1 n (%)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

Chromosome X

plot_flips(df_switch_x, "Beagle", "Eagle", "pop", "X")

Past versions of unnamed-chunk-145-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_x, "Beagle", "SHAPEIT", "pop", "X")

Past versions of unnamed-chunk-145-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flips(df_switch_x, "SHAPEIT", "Eagle", "pop", "X")

Past versions of unnamed-chunk-145-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

table_flip(df_switch_x, "pop")

Characteristic	AFR N = 2001	AMR N = 2001	EAS N = 2001	EUR N = 2001	SAS N = 2001
b_l_e
FALSE	120 (60%)	107 (54%)	115 (58%)	112 (56%)	94 (47%)
TRUE	80 (40%)	93 (47%)	85 (43%)	88 (44%)	106 (53%)
b_l_s
FALSE	13 (6.5%)	29 (15%)	41 (21%)	21 (11%)	26 (13%)
TRUE	187 (94%)	171 (86%)	159 (80%)	179 (90%)	174 (87%)
e_l_b
FALSE	86 (43%)	105 (53%)	93 (47%)	95 (48%)	114 (57%)
TRUE	114 (57%)	95 (48%)	107 (54%)	105 (53%)	86 (43%)
e_l_s
FALSE	14 (7.0%)	30 (15%)	55 (28%)	37 (19%)	42 (21%)
TRUE	186 (93%)	170 (85%)	145 (73%)	163 (82%)	158 (79%)
s_l_b
FALSE	191 (96%)	174 (87%)	163 (82%)	180 (90%)	177 (89%)
TRUE	9 (4.5%)	26 (13%)	37 (19%)	20 (10%)	23 (12%)
s_l_e
FALSE	188 (94%)	171 (86%)	151 (76%)	167 (84%)	160 (80%)
TRUE	12 (6.0%)	29 (15%)	49 (25%)	33 (17%)	40 (20%)
1 n (%)

cross_meth_plot(df_switch_x, "Flips", plot_flips, "pop", "X")

Past versions of unnamed-chunk-145-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

Flip Rate

plot_flip_rate <- function(df, m1, m2, pop, chrom = 15){
  p <- df %>%
    mutate(Beagle = n_flip_beagle / n_hets,
         Eagle = n_flip_eagle / n_hets,
         SHAPEIT = n_flip_shapeit / n_hets) %>%
    ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
    geom_point() +
    geom_abline(slope = 1, intercept = 0) +
    ggtitle("Flip rate", paste0("Chromosome ", chrom)) +
    theme_classic() +
    xlab(m1) +
    ylab(m2) +
    labs(color="Population") +
    scale_color_manual(values = cbPalette)
  return(p)
}

plot_flip_rate_noth <- function(df, m1, m2, pop, chrom = 15){
  p <- df %>%
    mutate(Beagle = n_flip_b / n_het,
         Eagle = n_flip_e / n_het,
         SHAPEIT = n_flip_s / n_het) %>%
    ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
    geom_point() +
    geom_abline(slope = 1, intercept = 0) +
    ggtitle("Flip rate", paste0("Chromosome ", chrom)) +
    theme_classic() +
    xlab(m1) +
    ylab(m2) +
    labs(color="Population") +
    scale_color_manual(values = cbPalette)
  return(p)
}

Chromosome 1

chrom <- 1

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-147-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-147-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-147-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-147-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-147-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-147-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-147-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-147-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 2

chrom <- 2

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-148-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-148-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-148-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-148-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-148-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-148-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-148-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-148-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 3

chrom <- 3

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-149-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-149-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-149-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-149-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-149-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-149-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-149-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-149-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 4

chrom <- 4

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-150-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-150-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-150-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-150-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-150-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-150-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-150-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-150-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 5

chrom <- 5

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-151-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-151-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-151-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-151-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-151-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-151-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-151-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-151-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 6

chrom <- 6

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-152-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-152-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-152-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-152-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-152-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-152-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-152-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-152-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 7

chrom <- 7

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-153-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-153-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-153-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-153-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-153-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-153-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-153-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-153-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 8

chrom <- 8

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-154-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-154-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-154-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-154-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-154-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-154-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-154-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-154-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 9

chrom <- 9

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-155-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-155-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-155-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-155-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-155-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-155-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-155-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-155-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 10

chrom <- 10

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-156-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-156-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-156-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-156-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-156-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-156-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-156-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-156-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 11

chrom <- 11

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-157-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-157-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-157-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-157-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-157-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-157-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-157-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-157-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 12

chrom <- 12

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-158-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-158-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-158-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-158-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-158-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-158-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-158-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-158-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 13

chrom <- 13

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-159-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-159-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-159-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-159-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-159-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-159-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-159-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-159-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 14

chrom <- 14

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-160-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-160-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-160-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-160-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-160-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-160-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-160-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-160-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 15

chrom <- 15

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-161-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-161-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-161-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-161-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-161-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-161-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-161-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-161-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 16

chrom <- 16

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-162-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-162-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-162-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-162-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-162-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-162-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-162-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-162-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 17

chrom <- 17

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-163-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-163-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-163-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-163-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-163-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-163-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-163-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-163-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 18

chrom <- 18

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-164-1.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-164-2.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-164-3.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-164-4.png

Version	Author	Date
9548985	theandyb	2025-07-14
b3306a4	theandyb	2025-06-19

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-164-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-164-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-164-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-164-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 19

chrom <- 19

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-165-1.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-165-2.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-165-3.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-165-4.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-165-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-165-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-165-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-165-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 20

chrom <- 20

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-166-1.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-166-2.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-166-3.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-166-4.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-166-5.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-166-6.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-166-7.png

Version	Author	Date
9548985	theandyb	2025-07-14

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Past versions of unnamed-chunk-166-8.png

Version	Author	Date
9548985	theandyb	2025-07-14

Chromosome 21

chrom <- 21

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-167-1.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

Past versions of unnamed-chunk-167-2.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-167-3.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

Past versions of unnamed-chunk-167-4.png

Version	Author	Date
9548985	theandyb	2025-07-14

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Chromosome 22

chrom <- 22

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

Chromosome X

plot_flip_rate(df_switch_x, "Beagle", "Eagle", "pop", "X")

plot_flip_rate(df_switch_x, "Beagle", "SHAPEIT", "pop", "X")

plot_flip_rate(df_switch_x, "SHAPEIT", "Eagle", "pop", "X")

cross_meth_plot(df_switch_x, "Flips", plot_flip_rate, "pop", "X")

Session information

sessionInfo()

R version 4.5.1 (2025-06-13)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3;  LAPACK version 3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/New_York
tzcode source: system (glibc)

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] gridExtra_2.3   gtsummary_2.1.0 yaml_2.3.10     reactable_0.4.4
 [5] pander_0.6.6    lubridate_1.9.4 forcats_1.0.0   stringr_1.5.1  
 [9] dplyr_1.1.4     purrr_1.0.4     readr_2.1.5     tidyr_1.3.1    
[13] tibble_3.2.1    ggplot2_3.5.2   tidyverse_2.0.0 workflowr_1.7.1

loaded via a namespace (and not attached):
 [1] Rdpack_2.6.3        sandwich_3.1-1      rlang_1.1.5        
 [4] magrittr_2.0.3      git2r_0.33.0        multcomp_1.4-28    
 [7] compiler_4.5.1      getPass_0.2-4       callr_3.7.6        
[10] vctrs_0.6.5         pkgconfig_2.0.3     crayon_1.5.3       
[13] fastmap_1.2.0       backports_1.5.0     labeling_0.4.3     
[16] utf8_1.2.4          promises_1.3.2      rmarkdown_2.29     
[19] markdown_2.0        tzdb_0.5.0          ps_1.9.0           
[22] nloptr_2.2.1        bit_4.6.0           xfun_0.52          
[25] cachem_1.1.0        litedown_0.7        jsonlite_1.9.1     
[28] later_1.4.1         broom_1.0.7         parallel_4.5.1     
[31] R6_2.6.1            bslib_0.9.0         stringi_1.8.4      
[34] RColorBrewer_1.1-3  boot_1.3-31         jquerylib_0.1.4    
[37] numDeriv_2016.8-1.1 estimability_1.5.1  Rcpp_1.0.14        
[40] knitr_1.50          zoo_1.8-13          httpuv_1.6.15      
[43] Matrix_1.7-3        splines_4.5.1       timechange_0.3.0   
[46] tidyselect_1.2.1    rstudioapi_0.17.1   codetools_0.2-20   
[49] processx_3.8.6      lattice_0.22-6      lmerTest_3.1-3     
[52] withr_3.0.2         coda_0.19-4.1       evaluate_1.0.3     
[55] archive_1.1.12      survival_3.8-3      xml2_1.3.8         
[58] pillar_1.10.1       whisker_0.4.1       reformulas_0.4.1   
[61] generics_0.1.3      vroom_1.6.5         rprojroot_2.0.4    
[64] hms_1.1.3           commonmark_1.9.5    munsell_0.5.1      
[67] scales_1.3.0        minqa_1.2.8         xtable_1.8-4       
[70] glue_1.8.0          emmeans_1.11.0      tools_4.5.1        
[73] lme4_1.1-36         fs_1.6.5            mvtnorm_1.3-3      
[76] cowplot_1.1.3       rbibutils_2.3       crosstalk_1.2.1    
[79] cards_0.5.1         colorspace_2.1-1    nlme_3.1-167       
[82] cli_3.6.4           gt_0.11.1           gtable_0.3.6       
[85] reactR_0.6.1        sass_0.4.10         digest_0.6.37      
[88] pbkrtest_0.5.3      TH.data_1.1-3       htmlwidgets_1.6.4  
[91] farver_2.1.2        htmltools_0.5.8.1   lifecycle_1.0.4    
[94] httr_1.4.7          bit64_4.6.0-1       MASS_7.3-65